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hermanzhaozzzz · May 24, 2023 · 38a76d2 · 38a76d2
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commit 38a76d2
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Showing 30 changed files with 394 additions and 151,137 deletions.
diff --git a/.gitignore b/.gitignore
@@ -1,29 +1,40 @@
+# this project
+*.csv
+*.json
+
+
+##############
+# common project
+##############
+# python cache
+**/__pycache__/
+# spyder
+**/.spyproject/
+# jupyterlab meta
+**/.ipynb_checkpoints/
+# pycharm meta
+**/.idea/
+# vscode
+**/.vscode/
+# Rstudio history
+**/.Rhistory
+# macos meta
+**/.DS_Store
+**/.Trash/
+
+# snakemake configure
+**/.snakemake/
+samples.json
+# HEXO public
 /public/
-/.ipynb_checkpoints/
 /.deploy_git/
+# TexPad temp
 /.texpadtmp/
-/.Trash/
-/.snakemake/
-/tmpdir_*/
+# Polaris slurm system
 sna*.err
 sna*.out
 job.srp*
-.DS_Store
-.Rhistory
-.localized
 slurm-*.out
-/public/
-/.ipynb_checkpoints/
-/.deploy_git/
-/.texpadtmp/
-/.Trash/
-/.snakemake/
+# Others
 /tmpdir_*/
-sna*.err
-sna*.out
-job.srp*
-.DS_Store
-.Rhistory
-.localized
-slurm-*.out
-plots/.ipynb_checkpoints/
+.localized
diff --git a/Snakefile.cuffdiff.py → __back/Snakefile.cuffdiff.py b/Snakefile.cuffdiff.py → __back/Snakefile.cuffdiff.py
diff --git a/...ocol_from_ZXT/20220501-tsRNA-spike-norm.R → ...ocol_from_ZXT/20220501-tsRNA-spike-norm.R b/...ocol_from_ZXT/20220501-tsRNA-spike-norm.R → ...ocol_from_ZXT/20220501-tsRNA-spike-norm.R
diff --git a/PUS7_DE_analyis.R → __back/protocol_from_ZXT/PUS7_DE_analyis.R b/PUS7_DE_analyis.R → __back/protocol_from_ZXT/PUS7_DE_analyis.R
diff --git a/...0220428_tsRNA_15_50_tidy_RPM.VTRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.VTRNA.csv.gz b/...0220428_tsRNA_15_50_tidy_RPM.VTRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.VTRNA.csv.gz
diff --git a/...20220428_tsRNA_15_50_tidy_RPM.YRNA.csv.gz → ...20220428_tsRNA_15_50_tidy_RPM.YRNA.csv.gz b/...20220428_tsRNA_15_50_tidy_RPM.YRNA.csv.gz → ...20220428_tsRNA_15_50_tidy_RPM.YRNA.csv.gz
diff --git a/...0220428_tsRNA_15_50_tidy_RPM.miRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.miRNA.csv.gz b/...0220428_tsRNA_15_50_tidy_RPM.miRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.miRNA.csv.gz
diff --git a/...0220428_tsRNA_15_50_tidy_RPM.snRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.snRNA.csv.gz b/...0220428_tsRNA_15_50_tidy_RPM.snRNA.csv.gz → ...0220428_tsRNA_15_50_tidy_RPM.snRNA.csv.gz
diff --git a/...20428_tsRNA_15_50_tidy_RPM.spikein.csv.gz → ...20428_tsRNA_15_50_tidy_RPM.spikein.csv.gz b/...20428_tsRNA_15_50_tidy_RPM.spikein.csv.gz → ...20428_tsRNA_15_50_tidy_RPM.spikein.csv.gz
diff --git a/...tsRNA_15_50_tidy_readsnumber.VTRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.VTRNA.csv.gz b/...tsRNA_15_50_tidy_readsnumber.VTRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.VTRNA.csv.gz
diff --git a/..._tsRNA_15_50_tidy_readsnumber.YRNA.csv.gz → ..._tsRNA_15_50_tidy_readsnumber.YRNA.csv.gz b/..._tsRNA_15_50_tidy_readsnumber.YRNA.csv.gz → ..._tsRNA_15_50_tidy_readsnumber.YRNA.csv.gz
diff --git a/...tsRNA_15_50_tidy_readsnumber.miRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.miRNA.csv.gz b/...tsRNA_15_50_tidy_readsnumber.miRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.miRNA.csv.gz
diff --git a/...tsRNA_15_50_tidy_readsnumber.snRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.snRNA.csv.gz b/...tsRNA_15_50_tidy_readsnumber.snRNA.csv.gz → ...tsRNA_15_50_tidy_readsnumber.snRNA.csv.gz
diff --git a/...RNA_15_50_tidy_readsnumber.spikein.csv.gz → ...RNA_15_50_tidy_readsnumber.spikein.csv.gz b/...RNA_15_50_tidy_readsnumber.spikein.csv.gz → ...RNA_15_50_tidy_readsnumber.spikein.csv.gz
diff --git a/..._tsRNA_15_50_tidy_readsnumber.tRNA.csv.gz → ..._tsRNA_15_50_tidy_readsnumber.tRNA.csv.gz b/..._tsRNA_15_50_tidy_readsnumber.tRNA.csv.gz → ..._tsRNA_15_50_tidy_readsnumber.tRNA.csv.gz
diff --git a/..._ZXT/tsRNA/20220501-tsRNA-spike-norm.R.gz → ..._ZXT/tsRNA/20220501-tsRNA-spike-norm.R.gz b/..._ZXT/tsRNA/20220501-tsRNA-spike-norm.R.gz → ..._ZXT/tsRNA/20220501-tsRNA-spike-norm.R.gz
diff --git a/...rom_ZXT/tsRNA/20220503-tsRNA-spikein.R.gz → ...rom_ZXT/tsRNA/20220503-tsRNA-spikein.R.gz b/...rom_ZXT/tsRNA/20220503-tsRNA-spikein.R.gz → ...rom_ZXT/tsRNA/20220503-tsRNA-spikein.R.gz
diff --git a/...NA/cutoff_RPM50_e12_correlation_W2.pdf.gz → ...NA/cutoff_RPM50_e12_correlation_W2.pdf.gz b/...NA/cutoff_RPM50_e12_correlation_W2.pdf.gz → ...NA/cutoff_RPM50_e12_correlation_W2.pdf.gz