A. Domingues adomingues
adomingues
/ deseq_zero_counts.Rmd
Created
May 8, 2023 15:50
Re-analysis of a dataset which strange differential expressed genes
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| ```{r } | |
| library("recount3") | |
| library("data.table") | |
| library("magrittr") | |
| library("DESeq2") | |
| rse <- recount3::create_rse_manual( | |
| project = "ERP010060", | |
| project_home = "data_sources/sra", | |
| organism = "human", |
adomingues
/ hg_to_git_conversion_draft.sh
Created
December 25, 2020 12:54
Convert hg (mercurial) to git repos
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| find . -maxdepth 2 -name ".hg" -type d | |
| ## convert hg to git | |
| pip install mercurial ## apt install did not work with the conversion tool | |
| ## install conversion tool | |
| mkdir -p ~/bin | |
| cd ~/bin/ | |
| git clone https://github.com/frej/fast-export.git |
adomingues
/ list_repos_with_branches.sh
Created
December 24, 2020 13:20
crawl all sub-directories wich are git repos and list those with more than one branch
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| parent=$(pwd) | |
| for repo in $(find ${parent} -maxdepth 2 -name ".git" -type d | sed 's/.git//'); do | |
| cd ${repo} | |
| n=$(git branch | wc -l) | |
| if [[ ${n} -gt 1 ]]; then | |
| echo ${repo} | |
| fi | |
| cd ${parent} | |
| done |
adomingues
/ add_password_to_ssh_keys.sh
Created
May 28, 2020 08:26
Add a password to an OpenSSH private key generated without a password
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| cd .ssh/ | |
| mkdir -p ~/.ssh/backup_keys | |
| ## backup current keys just in case | |
| for k in id_*; do | |
| cp $k backup_keys/$k"_bak_$(date +"%m_%d_%Y")" | |
| done | |
| ## it will ask for a password for every key file | |
| for k in $(ls id_* | grep -v pub); do |
adomingues
/ session_info_derfinder_10092019.R
Created
September 10, 2019 21:50
Session info for an issue
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| sessionInfo() R version 3.5.1 (2018-07-02) | |
| Platform: x86_64-pc-linux-gnu (64-bit) | |
| Running under: Debian GNU/Linux 9 (stretch) | |
| Matrix products: default | |
| BLAS: /fsimb/common/tools/R/3.5.1/lib/R/lib/libRblas.so | |
| LAPACK: /fsimb/common/tools/R/3.5.1/lib/R/lib/libRlapack.so | |
| locale: | |
| [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C |
adomingues
/ session_info_bioC_16072019.R
Created
July 18, 2019 13:12
session info for bioC question 16.07.2019
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| sessionInfo() | |
| R version 3.6.0 (2019-04-26) | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| Running under: macOS Mojave 10.14.5 | |
| Matrix products: default | |
| BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib | |
| locale: |
adomingues
/ .Rprofile
Last active
July 12, 2019 08:49
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| ## set default repository | |
| options(repos = "http://cran.rstudio.com") | |
| ## install packages if missing | |
| suppressMessages(if (!require("devtools")) utils::install.packages("devtools")) | |
| suppressMessages(if (!require("rdoc")) devtools::install_github("mdequeljoe/rdoc")) | |
| suppressMessages(if (!require("prettycode")) utils::install.packages("prettycode")) | |
| ## prettify the docs | |
| rdoc::use_rdoc() |
adomingues
/ readBAM.R
Created
January 3, 2019 09:13
— forked from SamBuckberry/readBAM.R
Import a bam file into R
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| # install the Rsamtools package if necessary | |
| source("http://bioconductor.org/biocLite.R") | |
| biocLite("Rsamtools") | |
| # load the library | |
| library(Rsamtools) | |
| # specify the bam file you want to import | |
| bamFile <- "test.bam" |
adomingues
/ session_info.R
Created
December 3, 2018 12:25
session info for collapseReplicates question
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| R version 3.5.1 (2018-07-02) | |
| Platform: x86_64-pc-linux-gnu (64-bit) | |
| Running under: Ubuntu 16.04.5 LTS | |
| Matrix products: default | |
| BLAS: /usr/lib/libblas/libblas.so.3.6.0 | |
| LAPACK: /usr/lib/lapack/liblapack.so.3.6.0 | |
| locale: | |
| [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C |
adomingues
/ deseq2_factors.R
Created
December 3, 2018 12:20
BioC question re factor levels after collapseReplicates
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| samples <- structure(list(sample = structure(c(3L, 4L, 5L, 6L, 7L, 8L, 9L, | |
| 10L, 1L, 2L, 14L, 14L, 15L, 16L, 17L, 18L, 19L, 20L, 20L, 21L, | |
| 22L, 23L, 23L, 24L, 25L, 11L, 12L, 13L), .Label = c("wt_Fish_10dpf_rep1_mRNA", | |
| "wt_Fish_10dpf_rep2_mRNA", "wt_Fish_1dpf_rep1_mRNA", "wt_Fish_1dpf_rep2_mRNA", | |
| "wt_Fish_2dpf_rep1_mRNA", "wt_Fish_2dpf_rep2_mRNA", "wt_Fish_3dpf_rep1_mRNA", | |
| "wt_Fish_3dpf_rep2_mRNA", "wt_Fish_6dpf_rep1_mRNA", "wt_Fish_6dpf_rep2_mRNA", | |
| "wt_PGCs_10dpf_rep1_mRNA", "wt_PGCs_10dpf_rep2_mRNA", "wt_PGCs_10dpf_rep3_mRNA", | |
| "wt_PGCs_1dpf_rep1_mRNA", "wt_PGCs_1dpf_rep2_mRNA", "wt_PGCs_1dpf_rep3_mRNA", | |
| "wt_PGCs_2dpf_rep1_mRNA", "wt_PGCs_2dpf_rep2_mRNA", "wt_PGCs_2dpf_rep3_mRNA", | |
| "wt_PGCs_3dpf_rep1_mRNA", "wt_PGCs_3dpf_rep2_mRNA", "wt_PGCs_3dpf_rep3_mRNA", |
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