20211113

Contents

1. Working directories
2. SYBR Green I alternative
3. Bible
1. 3.1. 本站网盘所有文件下载 ‖ 美地之声
4. 本站网盘所有文件下载
1. 4.1. [网盘下载] 圣经恢复本中英对照版PDF及EPUB文件合集 - 资源分享 - 中福论坛 - Powered by Discuz!
2. 4.2. Bible Rain – Bible is the rain of life.
5. eBook viewer
6. URL
1. 6.1. Chromium

Working directories

cd /media/ht/ht_5T_9/YouTubes/IT/Not_Classified/20211114 # to be organized
# 
i=/media/ht/ht_5T/Work/Projects/CC_n_HPV/RCA_Project/Real_Time_RCA/SYTO-13_sum.xlsx; \
setsid wps ${i}
# 
cd /media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20211117/3/Input_Doc
#######################################################################
# to be organized
# 
cd /media/ht/ht_5T_9/YouTubes/Science/Not_Classified/20210701
cd /media/ht/ht_5T_9/YouTubes/IT/Not_Classified/20211114/1
# i=/media/ht/ht_5T/Work/Funding/2021_十四五/Guidances/Satellite/2_指南编制说明_20211120_闫修订.docx; \
setsid wps ${i}

SYBR Green I alternative

Bible

本站网盘所有文件下载 ‖ 美地之声

本站网盘所有文件下载

2017-08-01 157705

提示：凡是电脑访问进入网盘，点开文件夹，发现文件顺序乱，点列表顶端的“文件名”或“日期”调序。

1、少数文件要填写提取码才能访问（提取码在括弧中）；访问百度网盘，非登录会员，请选“普通下载”。

2、百度网盘文件，若需批量下载，最好注册个百度帐号，登录，再一键转存到自己网盘，速度快比火箭，随用随取。

3、凡是歌谱文件，请下载后打开，因网盘在线阅览模糊；本站尽量将单首歌谱以压缩文件形式上传。

4、苹果系统设备，不再提供下载指引，因以往方法无效，APP下架，建议国内还是用安卓系统。

●诗歌类：

大本诗歌（mdzs）、大本诗歌领唱版（6vn5）、补充诗歌、新歌颂咏

标语诗歌、诗歌拾遗、英文诗歌、

**儿童信息汇总**（bbaw）：

（儿童诗歌、儿童经文诗歌、儿童英文44首、儿童18首）

●诗歌歌谱**：**

大本诗歌PDF、大本诗歌-繁PDF、新歌颂咏、新歌颂咏-繁PDF

诗歌拾遗、补充本PDF、补充本-繁PDF、补充新增本2012

补充本新增诗歌、标语歌谱、补充本PPT、诗歌修正版、儿童诗歌（ytfj）

●歌词类：

诗歌歌词CHM、路中人CHM、诗歌带搜索PDB

●MP3朗读：

旧约圣经恢复本朗读（提取码 cfd6）、新约圣经恢复本朗读（提取码 y8co）

旧约生命读经MP3（提取码 ry6g）、新约生命读经MP3（提取码 tpg4）

●书籍类：

书报合集、CHM格式、PDB格式、DOC格式、PDF格式、TXT格式

●圣经类：

恢复本圣经CHM、恢复本带注解PDB、恢复本中英对照CHM、恢复本中英对照PDB

新约圣经带注解CHM、圣经投影版CHM、圣经1000句CHM、新约圣经52题PDF

新约圣经读经指引EXE、希腊文圣经CHM、圣经金句

●生命读经：

生命读经CHM、生命读经PDB、英文新约生命读经PDF

旧约生命读经TXT、新约生命读经TXT

●影音类：

语音信息、福音问答六十题、福音短片、影音视频

●软件应用：

Epub文件、圣经各版本下载

注：网盘分享链接有时会失效，若遇问题，请联系，以便及时更新。

[网盘下载] 圣经恢复本中英对照版PDF及EPUB文件合集 - 资源分享 - 中福论坛 - Powered by Discuz!

将圣经恢复本的EPUB文件和各种格式的PDF文件打包在一起，方便下载。更新时间：2013.08.09
PDF文件因不方便缩放字号，所以专为iPad,iPhone,Galaxy S4,tablets等不同屏幕大小比例制作了不同的PDF文件。

圣经恢复本简体中英对照版文件全集。包括新旧约，经文版。均带有各卷各章书签。文件大小约40MB
http://www.biblerain.com/wp-content/uploads/2013/08/biblerain_sChnEngBible_v20130809.zip

包括：2个EPUB文件, 3个PDF文件
rev-Bib-sChn_v20130807.epub
rev-Bib-sChnEng_v20130807.epub
sceBib_iPad-14pt_20130807.pdf
sceBib_prn8pt_a4_20130807.pdf
sceBib_tablets-16pt_20130807.pdf

圣经恢复本繁体中英对照版文件全集。包括新旧约，经文版。均带有各卷各章书签。文件大小约40MB。包括：2个EPUB文件, 3个PDF文件
http://www.biblerain.com/wp-content/uploads/2013/08/biblerain_tChnEngBible_v20130809.zip

圣经恢复本简体中文版文件全集。包括新旧约，经文版。均带有各卷各章书签。包括：2个EPUB文件,6个PDF文件,3个TXT文件
http://www.biblerain.com/wp-content/uploads/2013/08/biblerain_sChnBible_v20130809.zip

圣经恢复本繁体中文版文件全集。包括新旧约，经文版。均带有各卷各章书签。包括：2个EPUB文件,6个PDF文件,3个TXT文件
http://www.biblerain.com/wp-content/uploads/2013/08/biblerain_tChnBible_v20130809.zip

欢迎访问www.biblerain.com查看更多。

Praise the Lord!

Bible Rain – Bible is the rain of life.

Bible Download (Recovery Version in English). 圣经恢复本英文版文件下载。

圣经中文和合本恢复本对照版下载 Holy Bible, Chinese Union Version and Recovery Version – Parallel Edition 2016.05.24

圣经恢复本Kindle版合集下载 – Bible for Kindle

专为Amazon Kindle制作。合集包含简体中文版，繁体中文版，简体中英对照版，繁体中英对照版和英文版MOBI文件。另包括:和合本圣经简体中文版，圣经恢复本简体中文带注解版文件。共7个文件。更新日期：2015.12.30。

圣经恢复本合集最新文件下载 – Bible for Smartphones, iPad and tablets.

分别专为智能手机，iPad和平板电脑tablets制作。合集包含简体中文版，繁体中文版，简体中英对照版，繁体中英对照版和英文版PDF文件和EPUB文件。说明。更新日期：2014.05.09

圣经智能手机版合集.zip – Bible for Smartphones
圣经iPad版合集.zip – Bible for iPad
圣经平板电脑版合集.zip – Bible for tablets

1. 圣经恢复本合集下载。更新日期：2013.08.09

2. 圣经恢复本中英文对照版。更新日期：2013.08.09

3. 圣经恢复本简体中文版文档。更新日期：2013.03.28

4. 聖經恢復本繁體中文版文檔。更新日期：2013.03.28

5. 圣经恢复本有声版，智能搜索，及中英对照

提后 3:15 并且知道你是从小明白圣经；这圣经能使你借着相信基督耶稣，有得救的智慧。

诗 105:41 祂打开磐石，水就涌出；在干旱之处，水流成河。

本站宗旨：通过提供圣经下载，在线圣经阅读，在线圣经搜索，及对圣经的归纳整理，以帮助和鼓励人们一同来读圣经，一同认识圣经里所启示的。

中文圣经恢复本，由**水流职事站出版，是翻译精准，且信达雅的中文圣经译本。圣经恢复本简介，请参看这里。圣经恢复本原文全部内容，已经由台湾福音书房向公众公开，请访问网上圣经网站**。

本站基于单纯朴素之帮助读者的目的，将圣经恢复本网络版的新旧约所有经文内容，整理成为文本格式，EPUB格式，PDF格式，和适合在Kindle上阅读的MOBI格式。经文内容经过认真校对，与中文圣经恢复本网络版完全一致。本站所提供的圣经恢复本文件，因时间能力有限，只包括圣经经文，不包括注解，敬请留意。

中文圣经恢复本 EPUB文件。更新日期：2013.08.09

包括新旧约。经文版。采用通行的EPUB格式，阅读方便，适用于各种平台包括手机，电子书阅读器，PC等。在苹果iOS上可用Blio或iBooks打开。

点击下载EPUB简体字版: rev-Bib-sChn_v20130807.epub

点击下载EPUB繁体字版: rev-Bib-tChn_v20130807.epub

中文圣经恢复本，方正准圆字体，PDF文件。更新日期：2013.03.28

经文版，包含新旧约。均带有各卷各章书签，可跳转。方正准圆字体。字号为30pt，22pt(二号)及8pt三种。

圣经恢复本中文简体30pt大字版1。为iPhone5,GalaxyS4等(16:9屏幕)特制：scBible_30pt_iPhone5-GalaxyS4.pdf

圣经恢复本中文简体30pt大字版2。为iPhone4,iPhone4S等(3:2屏幕)特制：scBible_30pt_for-iPhone4S.pdf

圣经恢复本中文简体22pt大字版1。为Apple iPad系列1-4代(4:3屏幕)特制：scBible_22pt_for-iPad1-4.pdf

圣经恢复本中文简体22pt大字版2。为Tablets, Kindle等(16:10屏幕)特制：scBible_22pt_for-Tablets.pdf

圣经恢复本中文简体8pt打印版。A4纸。仅570页：scBible_8pt_a4_Print-out.pdf

圣经恢复本中文简体8pt打印版。letter纸。仅604页：scBible_8pt_letter_Print-out.pdf

—

圣经恢复本中文繁体30pt大字版1。为iPhone5,GalaxyS4等(16:9屏幕)特制：tcBible_30pt_iPhone5-GalaxyS4.pdf

圣经恢复本中文繁体30pt大字版2。为iPhone4,iPhone4S等(3:2屏幕)特制：tcBible_30pt_for-iPhone4S.pdf

圣经恢复本中文繁体22pt大字版1。为Apple iPad系列1-4代(4:3屏幕)特制：tcBible_22pt_for-iPad1-4.pdf

圣经恢复本中文繁体22pt大字版2。为Tablets, Kindle等(16:10屏幕)特制：tcBible_22pt_for-Tablets.pdf

圣经恢复本中文繁体8pt打印版。A4纸。仅570页：tcBible_8pt_a4_Print-out.pdf

圣经恢复本中文繁体8pt打印版。letter纸。仅604页：tcBible_8pt_letter_Print-out.pdf

中文圣经恢复本文本TXT文件。较适于搜索，或在网络浏览器上直接阅读。这是其他所有格式版本的母版。更新日期：2013.03.07

圣经阅读辅助文件下载

1. 圣经恢复本各章首句和末句TXT文件

2. 圣经恢复本各章首句TXT文件

3. 圣经恢复本新旧约各卷书纲目TXT文件

圣经恢复本各章经节数统计表

[版本1下载] [版本2下载]

圣经读经记录表可以自己打勾的PDF文件，可用Foxit Reader 打开并保存

[中文版下载] [英文版下载]

圣经各章标记表

[版本1下载] [版本2下载] [TXT文件下载]

7. 圣经恢复本经节标记表 PDF文件

8. 圣经各卷书中英文对照表

圣经恢复本 WordNet Project

圣经的十二层维度：
标点(123,767) – 字(960,714) – 词 – 词组及短语 – 分句(117,031) – 句子(31,816)及经节(31,103) – 段落(6087) – 纲要段落(2719) – 章(1189) – 卷(66) – 按卷归类 – 全本圣经(1)

中文圣经恢复本，宋体字，PDF手机版文件。更新日期：2013.03.09

经文版，包含新旧约。均带有各卷各章书签，可跳转。宋体字。字号为22pt(二号)及18pt(小二号)。在iOS上建议使用Adobe Reader阅读，该App支持分层书签，跳转方便。或用Apabi Reader，Dropbox内嵌Reader也可以。

点击下载PDF手机简体字版,宋体22pt: scBib_22pt_v20130309.pdf

点击下载PDF手机繁体字版,宋体22pt: tcBib_22pt_v20130309.pdf

点击下载PDF手机简体字版,宋体18pt: scBib_18pt_v20130309.pdf

点击下载PDF手机繁体字版,宋体18pt: tcBib_18pt_v20130309.pdf

中文圣经恢复本经文版，宋体字，PDF文件，包含新旧约。均带有各卷各章书签，可跳转。更新日期：2013.02.27

scBib_9pt_a4_v20130227.pdf: 中文简体版。字体宋体9pt。中文小五号字体。666页。A4纸。

scBib_9pt_ltr_v20130227.pdf: 中文简体版。字体宋体9pt。中文小五号字体。701页。letter纸。

scBib_10pt5_a4_v20130227.pdf: 中文简体版。字体宋体10.5pt。中文五号字体。909页。A4纸。

scBib_10pt5_ltr_v20130227.pdf: 中文简体版。字体宋体10.5pt。中文五号字体。959页。letter纸。

tcBib_9pt_a4_v20130227.pdf: 中文繁体版。字体宋体9pt。中文小五号字体。765页。A4纸。

tcBib_10pt5_a4_v20130227.pdf: 中文繁体版。字体宋体10.5pt。中文五号字体。942页。A4纸。

All the contents in biblerain.com are only for non-commercial use. Any commercial uses are strictly prohibited.

eBook viewer

URL

Chromium

Expand all items >>

20211103

Contents

1. Working directories
2. Fix broken JPEG
3. A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection | Nature Immunology
4. A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection
1. 4.1. Abstract
5. R/CRAN update
6. PCR Efficiency
7. Rename
8. URL
1. 8.1. Chromium/X1
2. 8.2. Google Chrome/X1

Working directories

cd /media/ht/ht_5T/Work/肿瘤室工作/教育部论文评审
# 
cd /media/ht/ht_5T_10/eBooks/Masterpiece/Quran
# 
#####################################################
# 
ffmpeg -i <input> -filter:v fps=fps=30 <output>

i=1.mp4
ffmpeg -i ${i} -filter:v fps=fps=5 ${i%.*}_Treated.mp4

ffmpeg -i input.mov -r 24 -y output.mov

i=1.mp4
ffmpeg -i ${i} -r 5 -y ${i%.*}_5.mp4

MP4Box -add test_track1.h264:fps=30 -new 2.mp4

MP4Box -add ${i}#video -raw 1 -new test; MP4Box -add test_track1.h264:fps=5 -new ${i%.mp4}_5FPS.mp4

-FileModifyDate

exiftool -d "%Y%m%d_%H%M%S"  -CreateDate sample.jpg

exiftool -d "%Y%m%d_%H%M%S"  -FileModifyDate *.*

find . -depth -execdir rename -v 's/[\[\]]+/\_/g' {} \;

find ./ -name "*_?.*" -depth -execdir rename -v 's/\_//' {} \;

exiftool -b -ThumbnailImage -w $HOME/recovered/%f_thumb.%e -ext JPG <input directory>

exiftool -b -ThumbnailImage -w $HOME/recovered/%f_thumb.%e -ext JPG ./

cd ~/recovered

Fix broken JPEG

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection | Nature Immunology

Perspective
Published: 18 October 2021

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

Nature Immunology (2021)Cite this article

Metricsdetails

Abstract

SARS-CoV-2 infections display tremendous interindividual variability, ranging from asymptomatic infections to life-threatening disease. Inborn errors of, and autoantibodies directed against, type I interferons (IFNs) account for about 20% of critical COVID-19 cases among SARS-CoV-2-infected individuals. By contrast, the genetic and immunological determinants of resistance to infection per se remain unknown. Following the discovery that autosomal recessive deficiency in the DARC chemokine receptor confers resistance to Plasmodium vivax, autosomal recessive deficiencies of chemokine receptor 5 (CCR5) and the enzyme FUT2 were shown to underlie resistance to HIV-1 and noroviruses, respectively. Along the same lines, we propose a strategy for identifying, recruiting, and genetically analyzing individuals who are naturally resistant to SARS-CoV-2 infection.

R/CRAN update

sudo dpkg -i /media/ht/ht_5T/Stored_Softs/Cross_Platform_Softs/CRAN/RStudio/Installers/Desktop/rstudio-2021.09.0-351-amd64.deb # RStudio Desktop updated
# 

install.packages(c("caret", "coin", "corpcor", "cpp11", "digest", "e1071", "fastICA", "future", "ipred", "knitr", "labelled", "libcoin", "lubridate", "mime", "parallelly", "party", "progressr", "questionr", "RcppArmadillo", "readr", "recipes", "rlang", "rmarkdown", "shiny", "stringi", "tidyr", "tinytex", "tzdb", "visNetwork", "vroom", "xfun"))
# 
install.packages(c("caret", "coin", "digest", "e1071", "fastICA", "ipred", "libcoin", "lubridate", "mime", "party", "RcppArmadillo", "readr", "recipes", "rlang", "stringi", "tidyr", "tzdb", "vroom", "xfun"))
# 
##############################################################
# 
for ( i in c("caret", "coin", "digest", "e1071", "fastICA", "ipred", "libcoin", "lubridate", "mime", "party", "RcppArmadillo", "readr", "recipes", "rlang", "stringi", "tidyr", "tzdb", "vroom", "xfun")) { cat(i, "\n=========================="); install.packages(i, dependencies = TRUE)}


# for ( i in c("caret", "coin", "digest", "e1071", "fastICA", "ipred", "libcoin", "lubridate", "mime", "party", "RcppArmadillo", "readr", "recipes", "rlang", "stringi", "tidyr", "tzdb", "vroom", "xfun")) { cat(i)}
# 
install.packages("flextable", dependencies = TRUE)
# 
sudo apt install libcurl # Shell command

PCR Efficiency

Rename

linux-shell: renaming files to creation time - Stack Overflow

URL

Chromium/X1

Google Chrome/X1

Expand all items >>

20211031

Contents

1. Working directories
2. URL

Working directories

cd /media/ht/ht_5T/Work/Projects/HQ2020
# 
find ./ -type f | ag '.doc' | wc -l # output, 110
# 
cd /media/ht/ht_5T_10/Image_n_Movie/Images/Not_Classified/20211102 # to be organized

URL

Two Column Layout, in Gist
SublimeText3 Fold/Unfold all methods - Stack Overflow, collapse (fold) selected lines in Sublime Text Editor 3

Expand all items >>

20211025

Contents

1. Working directories
2. 10.3 Other packages for creating tables | R Markdown Cookbook
1. 2.1. 10.3 Other packages for creating tables
  1. 2.1.1. References

Working directories

sudo aptitude upgrade -o APT::Get::Fix-Missing=true
# 
cd /media/ht/ht_5T/Work/Experiments/qPCR/Tianlong
rename 's/$/.0/'  20211026A.*
7z a 20211026A.7z 20211026A.*

10.3 Other packages for creating tables | R Markdown Cookbook

10.3 Other packages for creating tables

There are many other R packages that can be used to generate tables. The main reason that I introduced kable() (Section 10.1) and kableExtra (Section 10.2) is not that they are better than other packages, but because I’m familiar with only them.14 Next I will list the packages that I’m aware of but not very familiar with. You can check them out by yourself, and decide which one fits your purpose best.

flextable (Gohel 2021a) and huxtable (Hugh-Jones 2021): If you are looking for a table package that supports the widest range of output formats, flextable and huxtable are probably the two best choices. They all support HTML, LaTeX, and Office formats, and contain most common table features (e.g., conditional formatting). More information about flextable can be found at https://davidgohel.github.io/flextable/, and the documentation of huxtable is at https://hughjonesd.github.io/huxtable/.
gt (Iannone, Cheng, and Schloerke 2021): Allows you to compose a table by putting together different parts of the table, such as the table header (title and subtitle), the column labels, the table body, row group labels, and the table footer. Some parts are optional. You can also format numbers and add background shading to cells. Currently gt mainly supports HTML output.15 You can find more information about it at https://gt.rstudio.com.
formattable (Ren and Russell 2021): Provides some utility functions to format numbers (e.g., percent() and accounting()), and also functions to style table columns (e.g., format the text, annotate numbers with background shading or color bars, or add icons in cells). Like gt, this package also primarily supports the HTML format. You can find more information about it from its GitHub project at https://github.com/renkun-ken/formattable.
DT (Xie, Cheng, and Tan 2021): As its author, I think I’m familiar with this package, but I did not introduce it in a separate section because it only supports the HTML format. DT is built on top of the JavaScript library DataTables, which can turn a static table into an interactive table on an HTML page. You may sort, search, and paginate the table. DT also supports formatting the cells, works with Shiny to build interactive applications, and has included a large number of DataTables extensions (e.g., you may export the table to Excel, or interactively reorder columns). See the package repository for more information: https://github.com/rstudio/DT.
reactable (Lin 2020): Similar to DT, this package also creates interactive tables based on a JavaScript library. Frankly speaking, it looks better than DT in several aspects in my eyes (such as row grouping and aggregation, and embedding HTML widgets). Had reactable existed in 2015, I would not have developed DT. That said, reactable does not contain all the features of DT, so you may read its documentation and see which one fits your purpose better: https://glin.github.io/reactable/.
rhandsontable (Owen 2021): Also similar to DT, and has an Excel feel (e.g., you can edit data directly in the table). Visit https://jrowen.github.io/rhandsontable/ to learn more about it.
pixiedust (Nutter 2021): Features creating tables for models (such as linear models) converted through the broom package (Robinson, Hayes, and Couch 2021). It supports Markdown, HTML, and LaTeX output formats. Its repository is at https://github.com/nutterb/pixiedust.
stargazer (Hlavac 2018): Features formatting regression models and summary statistics tables. The package is available on CRAN at https://cran.r-project.org/package=stargazer.
xtable (Dahl et al. 2019): Perhaps the oldest package for creating tables—the first release was made in 2000. It supports both LaTeX and HTML formats. The package is available on CRAN at https://cran.r-project.org/package=xtable.

I’m not going to introduce the rest of packages, but will just list them here: tables (Murdoch 2020), pander (Daróczi and Tsegelskyi 2021), tangram (Garbett 2020), ztable (Moon 2021), and condformat (Oller Moreno 2020).

References

Dahl, David B., David Scott, Charles Roosen, Arni Magnusson, and Jonathan Swinton. 2019. Xtable: Export Tables to LaTeX or HTML. http://xtable.r-forge.r-project.org/.

Daróczi, Gergely, and Roman Tsegelskyi. 2021. Pander: An r Pandoc Writer. https://rapporter.github.io/pander/.

Garbett, Shawn. 2020. Tangram: The Grammar of Tables. https://github.com/spgarbet/tangram.

Gohel, David. 2021a. Flextable: Functions for Tabular Reporting. https://CRAN.R-project.org/package=flextable.

Hlavac, Marek. 2018. Stargazer: Well-Formatted Regression and Summary Statistics Tables.

Hugh-Jones, David. 2021. Huxtable: Easily Create and Style Tables for LaTeX, HTML and Other Formats. https://hughjonesd.github.io/huxtable/.

Iannone, Richard, Joe Cheng, and Barret Schloerke. 2021. Gt: Easily Create Presentation-Ready Display Tables.

Lin, Greg. 2020. Reactable: Interactive Data Tables Based on React Table.

Moon, Keon-Woong. 2021. Ztable: Zebra-Striped Tables in LaTeX and HTML Formats. https://github.com/cardiomoon/ztable.

Murdoch, Duncan. 2020. Tables: Formula-Driven Table Generation. https://r-forge.r-project.org/projects/tables/.

Nutter, Benjamin. 2021. Pixiedust: Tables so Beautifully Fine-Tuned You Will Believe It’s Magic. https://github.com/nutterb/pixiedust.

Oller Moreno, Sergio. 2020. Condformat: Conditional Formatting in Data Frames. http://github.com/zeehio/condformat.

Owen, Jonathan. 2021. Rhandsontable: Interface to the Handsontable.js Library. http://jrowen.github.io/rhandsontable/.

Ren, Kun, and Kenton Russell. 2021. Formattable: Create Formattable Data Structures.

Robinson, David, Alex Hayes, and Simon Couch. 2021. Broom: Convert Statistical Objects into Tidy Tibbles.

Sjoberg, Daniel D., Michael Curry, Margie Hannum, Joseph Larmarange, Karissa Whiting, and Emily C. Zabor. 2021. Gtsummary: Presentation-Ready Data Summary and Analytic Result Tables.

Xie, Yihui, Joe Cheng, and Xianying Tan. 2021. DT: A Wrapper of the JavaScript Library DataTables. https://github.com/rstudio/DT.

Frankly speaking, I rarely use tables by myself, so I’m not highly motivated to learn how to create sophisticated tables.↩︎
If you need the support for other output formats such as LaTeX and Word, the gtsummary package (Sjoberg et al. 2021) has made some extensions based on gt that look very promising: https://github.com/ddsjoberg/gtsummary.↩︎

Expand all items >>

20211021

Contents

1. Working directories
2. SIBA
3. SARS-CoV-2 Download
4. URL
5. NCBI database download
6. HSV-2 BWA with magicblast
7. COVID-19 data US
1. 7.1. Data from HHS

Working directories

# 
#######################################################################
# 
# not successful with the codes as below
# ETE3 installation in X1
/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/ETE3/Installers/Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
# 
export PATH=~/anaconda_ete/bin:$PATH;
conda install -c etetoolkit ete3 ete3_external_apps # with default updating
#################
# Check installation
ete3 version
ete3 build check
# magicblast install
axel https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.6.0/ncbi-magicblast-1.6.0-src.tar.gz
# UGENE Pro installation
cd /media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/UGENE/Installer
axel https://github.com/ugeneunipro/ugene/releases/download/40.1/ugene-40.1-linux-x86-64.tar.gz

SIBA

1
2
3

OK /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref/3_SIBA.pdf
cd /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref
ug /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref/3_Template.gb

SARS-CoV-2 Download

NCBI Virus
Select “Download” from “SARS-CoV-2 Data Hub”

URL

Virus-Host Database

NCBI database download

Using NCBI edirect to access data at NCBI | ComputationalGenomicsManual

1	einfo -email xxx@sdsu.edu -dbs \| sort

HSV-2 BWA with `magicblast`

1
2
3

subl /media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20191025/README.md
# 
i=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20191025/README.md; subl ${i}

Index RefSeq
BWA with 10 sequences

herpes simplex virus type 2 HSV-2 (taxid:10310)

cp /media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/NC_001798_HSV-2.fas /home/ht/Downloads/HSV-2/
grep -o 'N' HSV-2_Test.fas | wc -l # includes lots of N nt, in total 44470
# 
###########################################################
# Index
# file:///media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/magicblast_Learning.html#37_Align_FASTA_with_subject_sequence_instead_of_indexed_database
# 
cd ~/Downloads/HSV-2/DB
Input=NC_001798_HSV-2.fas
DatabaseName=HSV-2
makeblastdb -in ${Input} -dbtype nucl -parse_seqids -out ${DatabaseName}
# 
Ref=~/Downloads/HSV-2/DB/HSV-2
Seq=HSV-2_Test.fas
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
time magicblast -query ${Seq} -db ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的
# 
Ref=~/Downloads/HSV-2/DB/NC_001798_HSV-2.fas
Seq=HSV-2_Test.fas
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
time magicblast -query ${Seq} -subject ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的

real    0m3.335s
user    0m1.295s
sys    0m0.661s

BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam
time samtools sort $BAM > "${BAM%.bam}.sort.bam"
time samtools index "${BAM%.bam}.sort.bam"
# 
Ref=
Tablet "${BAM%.bam}.sort.bam"

COVID-19 data US

Data from HHS

Results matching topic of hhs covid-19 | Page 1 of 2 | HealthData.gov

Expand all items >>

20211013

Contents

1. Working directories
2. Open an Office document from Mac OSX terminal
1. 2.1. Open Google Chrome from Mac OSX terminal

Working directories

# 质粒整理
i=/media/ht/ht_5T/Bioinformatics/肿瘤室物料管理/质粒出入库制度
cd ${i}
# 
i=/media/ht/ht_5T/Bioinformatics/肿瘤室物料管理/质粒出入库制度/李颖质粒整理/李颖质粒表格
cd ${i}
# 
################################################################
# Tianlong
i=/media/ht/ht_5T/Work/Experiments/qPCR/Tianlong
cd ${i}
# 
i=/media/ht/ht_5T/Work/Experiments/qPCR/Tianlong/README.md; subl ${i}
cd /media/ht/ht_5T/Work/Experiments/qPCR/Tianlong/Analysis

Open an Office document from Mac OSX terminal

osascript -e 'tell application "Microsoft Word" to create new document'
osascript -e 'tell application "Microsoft Word" to create new document' -e 'actviate'
open /Applications/Microsoft\ Word.app
# 
open -a "Microsoft PowerPoint" <filename.ppt>
# 
open -a "Microsoft PowerPoint" <ppt file path>
# 
open -a "Microsoft Word" <filename.docx>
open -b com.microsoft.PowerPoint <filename>

Open Google Chrome from Mac OSX terminal

cd /Applications/Google\ Chrome.app/

#cd into hidden folder containing the actual executable

cd Contents/MacOS/

#Launch Chrome in a new tab

./Google\ Chrome -new-tab

Expand all items >>

20211009

Contents

1. Working directories
2. Chrome extension
3. Probe of RPA

Working directories

# HQ
cd /media/ht/ht_5T/Work/Projects/HQ2020/Contract/20211002/1
# Journal checks
cd /media/ht/ht_5T/Work/References/Important_Ref/Journal_Checks
setsid okular /media/ht/ht_5T/Work/References/Important_Ref/Journal_Checks/Vitamin_D_signaling_inhibits_HBV_activity_by_directly_targeting_the_HBV_Core_promoter.pdf

Chrome extension

Probe of RPA

TwistAmp fpg Oligonucleotide Forms | Support | TwistDx

Expand all items >>

20210929

Contents

1. Working directories
2. VeePN is back
3. QQ in Linux
4. add rename command in termux - YouTube
5. WINE installation
6. OpenVPN
1. 6.1. OpenVPN3Linux – OpenVPN Community
2. 6.2. Usage/OpenVPN3
7. URL

Working directories

VeePN is back

QQ in Linux

add rename command in termux - YouTube

CLI, not for batch renaming

WINE installation

Ubuntu 20.10 wine、微信、QQ安装教程_修谭的博客-CSDN博客

#如果你使用的是64位Ubuntu，则先要开启32位安装环境：
sudo dpkg --add-architecture i386
#然后需要下载一个PGP公钥以识别软件仓库：
wget -nc https://dl.winehq.org/wine-builds/Release.key
#添加公钥并添加软件源：
sudo apt-key add Release.key
sudo apt-add-repository https://dl.winehq.org/wine-builds/ubuntu/
#更新软件列表
sudo apt-get update
#之后就可以选择Wine版本安装了： （选一种）
#稳定版（Stable branch）安装命令
sudo apt-get install --install-recommends winehq-stable
#开发版（Development branch)安装命令
sudo apt-get install --install-recommends winehq-devel
#发布版（Staging branch）安装命令
sudo apt-get install --install-recommends winehq-staging
#
###################################################################
#
备注：在执行sudo apt-get update时，可能会报错如下：
# 
W: GPG 错误：https://dl.winehq.org/wine-builds/ubuntu groovy InRelease: 由于没有公钥，无法验证下列签名： NO_PUBKEY 76F1A20FF987672F

解决办法：

sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys 76F1A20FF987672F
注意最后一串数字字母改成自己的那个失效的：NO_PUBKEY 76F1A20FF987672F

————————————————
版权声明：本文为CSDN博主「修谭」的原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接及本声明。
原文链接：https://blog.csdn.net/qq_41548910/article/details/114751964

OpenVPN

OpenVPN3Linux – OpenVPN Community

# Installation
sudo apt install apt-transport-https
wget https://swupdate.openvpn.net/repos/openvpn-repo-pkg-key.pub
# Download https://swupdate.openvpn.net/repos/openvpn-repo-pkg-key.pub
sudo apt-key add openvpn-repo-pkg-key.pub
# 
# Download
# https://swupdate.openvpn.net/community/openvpn3/repos/openvpn3-focal.list
# 
sudo mv openvpn3-focal.list /etc/apt/sources.list.d/openvpn3.list
sudo apt update
sudo apt install openvpn3

Usage/OpenVPN3

ls *.ovpn
# 
i=
sudo openvpn3 session-start --config ${i}
# 
pgrep openvpn | xargs sudo kill -9

Free OpenVPN - Private free VPN servers in Thailand

URL

Expand all items >>

20210923

Contents

1. Working directories
2. URL
3. Philip White Board/TV
4. Swine genome
1. 4.1. Swine Genome Project
2. 4.2. Sus scrofa (pig) from NCBI Genome
  1. 4.2.0.1. Display Settings:
  2. 4.2.0.2. Send to:
4.3. Summary
4.4. Publications (limited to 20 most recent records)
4.5. Representative(genome information for reference and representative genomes)
4.6. Chromosomes
4.7. External Resources

Working directories

1 2	ls /media/ht/ht_5T_9/YouTubes/History/Wuhan/Video/US/NYT_20200527-1.mkv i=/media/ht/ht_5T_9/YouTubes/History/Wuhan/Video/US/NYT_20200527-1.mkv

URL

Philip White Board/TV

Manual
Remote keyboard
WiFi connection

Swine genome

Swine Genome Project

Swine Genome Project | Comparative Genomics

TheSwine Genome Sequencing Consortium (SGSC)was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome.

The SGSC’s mission is to advance biomedical research for animal production and health by the development of DNA based tools and products resulting from the sequencing of the swine genome.

A physical map of the swine genome was generated by an international collaboration of four laboratories, led by theWellcome Trust Sanger InstituteandDr. Lawrence Schookat the University of Illinois at Urbana-Champaign. Both high-throughput fingerprinting and BAC-end sequencing were used to provide the template for an integrated physical map of the whole pig genome.

A high-quality draft genome sequence for the pig (Sus scrofa) was published in Nature in 2012. The paper entitled “Analyses of pig genomes provide insight into porcine demography and evolution“ described the sequencing, analysis, and annotation of the draft genome sequence. In parallel, a series of companion papers was published in BMC journals.

The genome paper reports analyses not only of the reference genome of Duroc 2-14 (aka. TJ Tabasco), but also analyses of genomes of several wild boars and other domesticated pigs. The analyses revealed a deep phylogenetic split between European and Asian wild boars dating back ~1 million years. This observation, in part, provides final justification for the wide trait mapping crosses developed in the 1990s, especially between Western and Chinese breeds. It was argued at the time that Chinese and Western pigs were as genetically divergent as Mus musculus and Mus spretus, species of mice which had been extensively used in mouse genetics research. In effect, this judgment has been validated.

As observed in other genomes, genes encoding immune response functions show evidence of rapid evolution. The pig has the largest repertoire of functional olfactory receptor genes of any mammal sequenced to date – perhaps that is why they are effective hunters for truffles. There is evidence that genes involved in taste are located in pig evolutionary break points. Pigs can tolerate higher levels of substances that are distasteful to humans – perhaps the ability of pigs to eat material that is unpalatable to humans was one of the attractions when they were domesticated.

A comparison of multiple pig genomes and the comparison of pig and human genomes reveal several potentially disease-causing genetic variants which may extend the value of pigs in biomedical research.

The pig industry has an excellent track record for rapid and effective exploitation of new knowledge and technologies. The pig genome sequence is expected to enable the acceleration of pig genetics research, the results of which are expected to be translated into pig improvement in a timely manner. The pig industry support for the sequencing project is gratefully acknowledged by the Consortium.

This paper represents an important landmark for the Consortium. For many of the authors their collaborative research in pig genetics and genomics stretches back to the early 1990s and the European PiGMap project and USDA Pig Genome Coordinated activities in the US. The project has benefited from these long established collaborations and friendships. Trans-national funding was critical to the delivery of the project, including USDA funding to The Wellcome Trust Sanger Institute, European Commission and European Research Council funding, and significant contributions from Korean, Japanese, and Chinese national sources and many others.

Sus scrofa (pig) from NCBI Genome

Sequence data:

genome assemblies: 22; sequence reads: 35

(See Genome Assembly and Annotation report)

Statistics:

median total length (Mb): 2459.03

median protein count: 63577

median GC%: 41.5

NCBI Annotation Release:

106

Sus scrofa (pig)
Representative genome:Sus scrofa (assembly Sscrofa11.1)
Download sequences in FASTA format forgenome,transcript,protein
Download genome annotation inGFF,GenBankortabularformat
BLAST against Sus scrofagenome,transcript,protein
All 22 genomes for species:
Browse thelist
Download sequence and annotation fromRefSeqorGenBank
TryNCBI Datasets- a new way to download genome sequence and annotation we’re testing in NCBI Labs

Display Settings:

Overview

Send to:

ID: 84

Organism Overview;Genome Assembly and Annotation report [22];Organelle Annotation Report [6]


	Sus scrofa (pig) pig Lineage:Eukaryota[8059];Metazoa[3802];Chordata[1811];Craniata[1789];Vertebrata[1789];Euteleostomi[1773];Mammalia[480];Eutheria[455];Laurasiatheria[259];Artiodactyla[125];Suina[3];Suidae[2];Sus[1];Sus scrofa[1]

The pig (Sus scrofa) is a member of the artiodactyls, or cloven-hoofed mammals, which are an evolutionary clade distinct from the primates and rodents. Pigs exist in both feral and domesticated populations that have distinct phenotypes and karyotypes. The haploid genome of the domesticated pig is estimated to be 2800 Mb. The diploid genome isMore…

Summary

| Sequence data: | genome assemblies: 22; sequence reads: 35 | (See Genome Assembly and Annotation report) |


Statistics:	median total length (Mb): 2459.03
median protein count: 63577
median GC%: 41.5
NCBI Annotation Release:	106

Publications (limited to 20 most recent records)

The Meishan pig genome reveals structural variation-mediated gene expression and phenotypic divergence underlying Asian pig domestication.Zhou R, et al. Mol Ecol Resour 2021 Aug
An improved pig reference genome sequence to enable pig genetics and genomics research.Warr A, et al. Gigascience 2020 Jun 1
Molecular characterization of the complete mitochondrial genome sequence of Indian wild pig (Sus scrofa cristatus).Kumar Jadav K, et al. Anim Biotechnol 2019 Apr

More…

Representative(genome information for reference and representative genomes)

Reference genome:

minus sign Sus scrofa Sscrofa11.1

Submitter:The Swine Genome Sequencing Consortium (SGSC)

Type	Name	RefSeq	INSDC	Size (Mb)	GC%	Protein	rRNA	tRNA	Other RNA	Gene	Pseudogene
Chr	1	NC_010443.5	CM000812.5	274.33	40.2	5,392	-	21	1,255	2,423	260
Chr	2	NC_010444.4	CM000813.5	151.94	42.5	5,641	-	29	988	2,683	257
Chr	3	NC_010445.4	CM000814.5	132.85	44.2	4,054	-	36	941	1,805	109
Chr	4	NC_010446.5	CM000815.5	130.91	41.6	3,628	-	70	868	1,650	104
Chr	5	NC_010447.5	CM000816.5	104.53	42.2	3,219	-	12	653	1,458	103
Chr	6	NC_010448.4	CM000817.5	170.84	44.7	6,262	-	16	1,282	2,724	167
Chr	7	NC_010449.5	CM000818.5	121.84	43.1	3,720	-	143	889	1,978	133
Chr	8	NC_010450.4	CM000819.5	138.97	39.5	2,216	-	2	644	1,096	109
Chr	9	NC_010451.4	CM000820.5	139.51	41.2	3,659	-	8	893	1,715	169
Chr	10	NC_010452.4	CM000821.5	69.36	42.7	1,455	-	5	428	664	54
Chr	11	NC_010453.5	CM000822.5	79.17	40.6	1,156	-	5	406	559	43
Chr	12	NC_010454.4	CM000823.5	61.6	47.7	3,151	-	44	708	1,468	58
Chr	13	NC_010455.5	CM000824.5	208.34	39.9	4,724	-	4	918	1,841	200
Chr	14	NC_010456.5	CM000825.5	141.76	43.2	4,088	-	11	811	1,667	132
Chr	15	NC_010457.5	CM000826.5	140.41	39.9	2,727	-	7	561	1,106	115
Chr	16	NC_010458.4	CM000827.5	79.94	40.3	940	-	5	390	588	50
Chr	17	NC_010459.5	CM000828.5	63.49	44.7	1,823	-	5	459	821	46
Chr	18	NC_010460.4	CM000829.5	55.98	43.1	1,368	-	17	400	659	41
Chr	X	NC_010461.5	CM000830.5	125.94	40.4	2,482	-	8	523	1,172	170
Chr	Y	NC_010462.3	LT634572.1	43.55	47.5	118	-	-	57	147	45
	MT	NC_000845.1	-	0.02	39.5	13	2	22	-	37	-
Un	-	.	-	66.63	43.3	1,741	2	62	446	2,127	719

Chromosomes

Chr1: chromosome

Chr2: chromosome

Chr3: chromosome

Chr4: chromosome

Chr5: chromosome

Chr6: chromosome

Chr7: chromosome

Chr8: chromosome

Chr9: chromosome

Chr10: chromosome

Chr11: chromosome

Chr12: chromosome

Chr13: chromosome

Chr14: chromosome

Chr15: chromosome

Chr16: chromosome

Chr17: chromosome

Chr18: chromosome

ChrX: chromosome

ChrY: chromosome

Click on chromosome name to open Genome Data Viewer

External Resources

Expand all items >>

20210917

Contents

1. Working directories

Working directories

cd /media/ht/ht_5T/Work/Projects/Biosafety/Antibody
# 
cd /media/ht/ht_5T/Work/Projects/HQ2020/719所合作
# 
cd /media/ht/ht_5T/Work/Funding/2021_十四五/Application/Cell_Free/20210917
# 
cd /media/ht/ht_5T/Work/Projects/HPV/Ref

Expand all items >>

Working directories

SYBR Green I alternative

Bible

本站网盘所有文件下载

eBook viewer

URL

Chromium

Working directories

Fix broken JPEG

A global effort to dissect the human genetic basis of resistance to SARS-CoV-2 infection

Abstract

R/CRAN update

PCR Efficiency

Rename

URL

Chromium/X1

Google Chrome/X1

Working directories

URL

Working directories

References

Working directories

SIBA

SARS-CoV-2 Download

URL

NCBI database download

HSV-2 BWA with magicblast

COVID-19 data US

Data from HHS

Working directories

Open an Office document from Mac OSX terminal

Open Google Chrome from Mac OSX terminal

Working directories

Chrome extension

Probe of RPA

Working directories

VeePN is back

QQ in Linux

WINE installation

OpenVPN

Usage/OpenVPN3

URL

Working directories

URL

Philip White Board/TV

Swine genome

Swine Genome Project

Sus scrofa (pig) from NCBI Genome

Working directories

HSV-2 BWA with `magicblast`