First commit

.gitignore

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+.Rproj.user
+.Rprofile
+.Rhistory
+.RDataTmp
+*.RData
+*.rda
+*.pdf
+*.rds
+*.png
+*.svg
+.Ruserdata
+results/*
+renv/*
+slurm*
+run*
+data/*

README.md

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+# Repository for scripts used in *Gene- and transcript-level analyses reveal sex-specific trancriptional alterations in prefrontal cortex in Major Depressive Disorder*. 
+
+## Requisites
+
+We use Miniconda (or Anaconda) for environment management (See `environment.yml` file). To create the environment:
+`conda env create -f environment.yml`
+
+We use R version 4.1.2 and Bioconductor version 3.14.
+
+Here, we use multiple R packages. We use `renv` to track R package versions (see `renv.lock` file).
+
+Clone this repository to your local machine and open the project through `mdd.Rproj` to install required packages. 
+
+## Overall project structure
+
+This project is organized in the following directories:
+
+ - `data/`: Holds the RNA-seq processed data, study metadata, and genome references;
+ - `scripts/`: Holds all the scripts used in the analyses;
+ - `results/`: Holds results from each step analysis.
+
+ In each directory, there is detailed description of files. 
+
+
+
+
+
+

environment.yml

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+name: mdd-env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - _libgcc_mutex=0.1=conda_forge
+  - _openmp_mutex=4.5=1_gnu
+  - _r-mutex=1.0.1=anacondar_1
+  - binutils_impl_linux-64=2.36.1=h193b22a_2
+  - binutils_linux-64=2.36=hf3e587d_3
+  - bwidget=1.9.14=ha770c72_1
+  - bzip2=1.0.8=h7f98852_4
+  - c-ares=1.18.1=h7f98852_0
+  - ca-certificates=2021.10.8=ha878542_0
+  - cairo=1.16.0=ha00ac49_1009
+  - curl=7.80.0=h494985f_1
+  - font-ttf-dejavu-sans-mono=2.37=hab24e00_0
+  - font-ttf-inconsolata=3.000=h77eed37_0
+  - font-ttf-source-code-pro=2.038=h77eed37_0
+  - font-ttf-ubuntu=0.83=hab24e00_0
+  - fontconfig=2.13.1=hba837de_1005
+  - fonts-conda-ecosystem=1=0
+  - fonts-conda-forge=1=0
+  - freetype=2.10.4=h0708190_1
+  - fribidi=1.0.10=h36c2ea0_0
+  - gcc_impl_linux-64=9.4.0=h03d3576_11
+  - gcc_linux-64=9.4.0=h391b98a_3
+  - gettext=0.19.8.1=h73d1719_1008
+  - gfortran_impl_linux-64=9.4.0=h0003116_11
+  - gfortran_linux-64=9.4.0=hf0ab688_3
+  - graphite2=1.3.13=h58526e2_1001
+  - gsl=2.7=he838d99_0
+  - gxx_impl_linux-64=9.4.0=h03d3576_11
+  - gxx_linux-64=9.4.0=h0316aca_3
+  - harfbuzz=3.2.0=hb4a5f5f_0
+  - icu=69.1=h9c3ff4c_0
+  - jbig=2.1=h7f98852_2003
+  - jpeg=9d=h36c2ea0_0
+  - kernel-headers_linux-64=2.6.32=he073ed8_15
+  - krb5=1.19.2=h48eae69_3
+  - ld_impl_linux-64=2.36.1=hea4e1c9_2
+  - lerc=3.0=h9c3ff4c_0
+  - libblas=3.9.0=12_linux64_openblas
+  - libcblas=3.9.0=12_linux64_openblas
+  - libcurl=7.80.0=h494985f_1
+  - libdeflate=1.8=h7f98852_0
+  - libedit=3.1.20191231=he28a2e2_2
+  - libev=4.33=h516909a_1
+  - libffi=3.4.2=h7f98852_5
+  - libgcc-devel_linux-64=9.4.0=hd854feb_11
+  - libgcc-ng=11.2.0=h1d223b6_11
+  - libgfortran-ng=11.2.0=h69a702a_11
+  - libgfortran5=11.2.0=h5c6108e_11
+  - libglib=2.70.2=h174f98d_1
+  - libgomp=11.2.0=h1d223b6_11
+  - libiconv=1.16=h516909a_0
+  - liblapack=3.9.0=12_linux64_openblas
+  - libnghttp2=1.43.0=ha19adfc_1
+  - libopenblas=0.3.18=pthreads_h8fe5266_0
+  - libpng=1.6.37=h21135ba_2
+  - libsanitizer=9.4.0=h79bfe98_11
+  - libssh2=1.10.0=ha35d2d1_2
+  - libstdcxx-devel_linux-64=9.4.0=hd854feb_11
+  - libstdcxx-ng=11.2.0=he4da1e4_11
+  - libtiff=4.3.0=h6f004c6_2
+  - libuuid=2.32.1=h7f98852_1000
+  - libwebp-base=1.2.1=h7f98852_0
+  - libxcb=1.13=h7f98852_1004
+  - libxml2=2.9.12=h885dcf4_1
+  - libzlib=1.2.11=h36c2ea0_1013
+  - lz4-c=1.9.3=h9c3ff4c_1
+  - make=4.3=hd18ef5c_1
+  - ncurses=6.2=h58526e2_4
+  - openssl=3.0.0=h7f98852_2
+  - pango=1.48.10=h54213e6_2
+  - pcre=8.45=h9c3ff4c_0
+  - pcre2=10.37=h032f7d1_0
+  - pixman=0.40.0=h36c2ea0_0
+  - pthread-stubs=0.4=h36c2ea0_1001
+  - r-base=4.1.2=hde4fec0_0
+  - readline=8.1=h46c0cb4_0
+  - sed=4.8=he412f7d_0
+  - sysroot_linux-64=2.12=he073ed8_15
+  - tk=8.6.11=h27826a3_1
+  - tktable=2.10=hb7b940f_3
+  - xorg-kbproto=1.0.7=h7f98852_1002
+  - xorg-libice=1.0.10=h7f98852_0
+  - xorg-libsm=1.2.3=hd9c2040_1000
+  - xorg-libx11=1.7.2=h7f98852_0
+  - xorg-libxau=1.0.9=h7f98852_0
+  - xorg-libxdmcp=1.1.3=h7f98852_0
+  - xorg-libxext=1.3.4=h7f98852_1
+  - xorg-libxrender=0.9.10=h7f98852_1003
+  - xorg-libxt=1.2.1=h7f98852_2
+  - xorg-renderproto=0.11.1=h7f98852_1002
+  - xorg-xextproto=7.3.0=h7f98852_1002
+  - xorg-xproto=7.0.31=h7f98852_1007
+  - xz=5.2.5=h516909a_1
+  - zlib=1.2.11=h36c2ea0_1013
+  - zstd=1.5.1=ha95c52a_0

mdd.Rproj

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+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX