.cj_command

ls
ll
ls -al 
cd .Rproj.user/
l
cd /tmjp
cd /tmp/
ls
ll
ls -al
cd .Rproj.user/
l
cd ../
ls
ll
du -sh /home/*
du -sh /home/*|sort -h
du -sh /home/*|sort -hr
cd /home/cliu18
git status
git add -A
git commit -m 'regression analysis'
git push origin master
ps xf
l
exit
ls
leng2 /home/cliu18/liucj/github/RstudioWithGit/cjFun.R
ls
git status
git add -A
git commit -m 'add cjFun'
top
l
git push origin master
ls
cd mutationInPromoter
l
liucj
ls
git status
git add -A
git commit -m 'check PDE4DIP mutation'
git push origin master
breast
ls
git status
git add -a
git add -A
git commit -m "reanalysis BRCA
"
git push origin master
ps xf
cd mutationInPromoterB
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter
ls
git status
git add -A
git commit -m "brca reanalysis"
git push origin master
l
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter/BRCA/
ls
git status
git add -A
git commit -m "loadAnnoSomatic"
git push origin master
ls
cd mutationInPromoter
ls
cd mutationInPromoter
ls
cd mutationInPromoter
ls
cd mutationInPromoter
ls
cd mutationInPromoter/BRCA/
ls
git status
rm mutationInPromoter/BRCA/nohup.out.03
git status
ps xf
ls
0.
ls
cd mutationInPromoter
ls
git status
git push add -A
git push origin master
git add -A
git commit -m "somaticMutationAnalysis"
git push origin master
liucj
ls
cd mutationInPromoter/BRCA/
ls
git status
git add -A
git commit -m "getExpression"
git push origin master
ls
liucj
l
cd mutationInPromoter/BRCA/
l
cd mutationInPromoter/BRCA/
ls
git status
git add -
git add -A
git commit -m "gene expression"
git push origin master
ls
ps xf
ls
ls
cd mutationInPromoter/BRCA/
exit
ls
cd mutationInPromoter/BRCA/
ls
cd goodRCode/
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter/BRCA/
l
git status
git add -A
git commit -m "reanalysis"
git push origin master
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter/BRCA/
l
breast
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter
l
sll
ls
cd mutationInPromoter/BRCA/
ls
l
cd mutationInPromoter
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter/BRCA/
ls
git status
git add -A
git commit -m 'brca reanalysis summary'
git push origin master
l
ll
ls
liucj
ls
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter
ls
git status
git add -a
git add -A
git commit -m "brca reanalysis"
git push origin master
ls
exit
ls
ll
git status
git add mutationInPromoter/BRCA/06_1.geneExpression.R 
git commit -m "geneexpression"
git push origin master
cat /home/cliu18/.ssh/id_rsa
L
l
R
ipython
exit
ls
ll
l
df -h
ps xf
kill 42845
ls
df -h
cd /home/
ls
cd mutationInPromoter/BRCA/
ls
l
cd mutationInPromoter/BRCA/
ls
cd mutationInPromoter
l
ls
cd mutationInPromoter2/
l
cd mutationInPromoter
ls
ll
ls
cd mutationInPromoter
ls
ll
cd cistrome_data/
l
git status
git add -A
git commit -m "gene expression"
git push origin master
ls
ll
cd goodRCode/
l
ls
ll
ls
ll
cd ../
ls
ll
mkdir autophagy
ls
cd autophagy/
l
cd autophagy/
l
mv autophagy autophagy_codes
ls
ll
cd autophagy_codes/
l
git status
git add -A
git commit -m "new project autophagy-lysosome"
git push orgin master
git push origin master
ls
git status
git add -a
git add -A
l
ll
cd testCode/
l
ll
cd cjFun.R 
ls
ll
cd ../
ls
ll
l
ll
ls
ll
cd autophagy_codes/
ls
grep brca.fpkm.txt */*
grep brca.fpkm.txt */*/*
grep brca.fpkm.txt */*/*/*
grep brca.fpkm.txt */*/*/*/*
grep brca.fpkm.txt */*/*/*/*/*
grep brca.fpkm.txt */*/*/*/*/*/*
grep brca.fpkm.txt */*/*/*/*/*/*/*
grep brca.fpkm.txt */*/*/*/*/*/*/*/*
grep brca.fpkm.txt *
grep brca.fpkm.txt */*
grep brca.fpkm.txt */*/*
ls
l
cd autophagy_codes/
l
git status
git add -A
git commit -m "autophagy expr"
git push origin master
ll
mv autophagy_codes/ye_circadian_code ../
ll
git status
git add -A
git commit -m "rm ye_code"
git push origin master
l
mv ../ye_circadian_code/ autophagy_codes/
l
cd autophagy_codes/
l
git status
echo autophagy_codes/ye_circadian_code >> .gitignore 
cat .gitignore 
exit
ls
ll
git status
cat .gitignore 
vim .gitignore 
ls
ll
cd ../
ls
ll
git status
exit
ls
l
git status
vim .gitignore 
cd ../
ls
ll
git status
git add autophagy_codes/01_expr/02_gene_list_expr_fc.R
git commit -m "mod 02"
git status
git push origin master
git status
l
exit
ls
ll
git status
cat .gitignore 
ls
ll
git status
git add -A
git commit -m "mod 02 r"
ls
git status
which leng
cat ~/liucj/scripts/leng
exit
exit
ls
l
cd autophagy_codes/
l
cd mutationInPromoter
ls
mv autophagy_codes/ye_circadian_code ../
ll
git status
git add -A
git commit -m "add 03"
git push origin master
ls
mv ../ye_circadian_code/ autophagy_codes/
git status
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
git status
git add autophagy_codes/01_expr/*
git commit -m "at details"
git push origin master
ls
ll
cd autophagy_codes/
l
git status
git add autophagy_codes/01_expr/.cj_command autophagy_codes/01_expr/03_a_atg_gene_list.R
git add autophagy_codes/01_expr/03_a_atg_gene_list.R autophagy_codes/01_expr/03_a_gene_expr.R autophagy_codes/01_expr/04_use_all_samples.R
ls
ll
vim .gitignore 
cd
l
git status
git add -A
ls
git status
git push origin master
ll
git status
git commit -m "add 03_gene_expr"
git push origin master
ls
ll
cat .gitignore 
ls
git status
git add A
git add -A
git status
git commit -m "03_a_gene_expr.R"
git push origin master
ls
ll
cd /extraspace/TCGA/TCGA_clinical/
ls
cd autophagy_codes/
l
cd mutationInPromoter
l
ll
find . -name "*.R"
find . -name "*.R"|grep -i "kruskal.test"
find . -name "*.r"|grep -i "kruskal.test"
find . -name "*.r"|grep -i "kruskal"
find . -name "*.R"|grep -i "kruskal"
top
ps xf
top
ll
git status
ls
ll
cd autophagy_codes/
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
git status
git add -A
git commit -m "survival"
git push origin master
git status
exit
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
git add -A
git commit -m "rppa'
git commit -m "rppa"
git push origin master
ls
ls
git status
git add -A
git status
git commit -m "rppa"
git push origin master
ls
les /extraspace/yye1/analysis/Circadian/RPPA/AllCancer_AllCir_pathwayScore_pvalue.final.csv
ll
ls
git status
l
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
cd ../
ls
git status
l
git add -A
git commit -m "expr"
git push origin master
l
ps xf
top
ll
cd
ls
ll
cd autophagy_codes/
ls
ll
git status
git add -A
git commit -m "hypoxia and cnv"
git push origin master
ls
cd
ls
cd autophagy_codes/
l
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
git status
git add -A
git commit -m "mutation and ccle drug"
git push origin master
ll
ls
ll
git status
ls
cd /extraspace/
ls
ll
git status
git add -A
git commit -m "ccle"
git push origin master
ll
ps xf
l
git status
git add -A
git commit -m "drug"
git push origin master
ps xf
l
ll
cd autophagy_codes/
l
ll
cd autophagy_codes/
ls
cd autophagy_codes/
l
git status
git add -A 
git commit -m "ctrp"
git push origin master
ps f
ll
l
ll
cd autophagy_codes/
ls
git status
git add -A
git commit -m "clle drug"
git push origin master
l
cd 
l
git status
ps xf
kill 16280
l
l
source ~/.profile
gs
ga -A
gs
gm 
gm "seminar change"
gs
gp
source ~/.profile
../
..
ll
ls
ll
cd autophagy_codes/
cd "/home/cliu18/liucj/projects/6.autophagy/TCGA"
l
git status
ga -A
gm "rppa name"
gp
ll
cd autophagy_codes/
l
ga -a
ga -A
gm "rppa name map"
gp
ll
cd autophagy_codes/
l
ga -A
gm "rppa nam "
gp
cd autophagy_codes/
l
gs
ga -A
gm "rppa symbol map"
gp
ls
l
cd autophagy_codes/
l
gs
ga -A
gs "rppa name map
"
gp
gm "rppa name map
"
gp
l
ll
cd
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
gs
ga -A
gm "mirna and methylation"
gp
ps xf
ll
l
cd 
sl
ll
cd autophagy_codes/
l
ll
gs
ga -A
gs
gm
gc "update data")
gc "update data"
gm "update data"
gp
ls
ll
cd autophagy_codes/
l
ll
ll /extraspace/liucj/projects/6.autophagy/
cd /extraspace/liucj/projects/6.autophagy/
ls
gs
ga -A
gm "mirna and methylation"
gp
ll
ls
ll
cd autophagy_codes/
ls
cd autophagy_codes/
ls
ll
gitr
ls
ll
rm iris.xlsx 
l
ll
rm r2excel_test.xlsx 
ll
l
ll
rm Mutation_count.xlsx 
l
ll
exit
ls
cd autophagy_codes/
ls
cd autophagy_codes/
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
ls
cd autophagy_codes/
ls
cd autophagy_codes/
ls
gs
git add -A
git status
git commit -m "coca"
git push origin master
ll
cd expr_matrix/
ls
ll
cd autophagy_codes/
ls
ll
cd autophagy_codes/
ls
git status
git add -A
git commit -m "coca+cor" 
rm autophagy_codes/01_expr/Rplots.pdf
ps xf
ll
git add -A
git status
git commit -m "coca + cor"
git push origin master
ll autophagy_codes/01_expr/Rplots.pdf
git push origin master
git status
git rm autophagy_codes/01_expr/Rplots.pdf
git log
git revert
git checkout master
git checkout commit
git log --oneline
git checkout aaab9ac
git status
git log -h
git log --oneline
git log --oneline|head
git checkout aaab9ac
git checkout master
git checkout aaab9a cautophagy_codes/01_expr/Rplots.pdf
git checkout 3b71338 cautophagy_codes/01_expr/Rplots.pdf
git checkout HEAD cautophagy_codes/01_expr/Rplots.pdf
git status
git log --oneline
git status
git add -A
git status
git commit -m "coca + corr"
git push origin master
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
cd
ls
ll
cd testCode/
l
ll
cd testCode/
l
cd ../
ls
cd autophagy_codes/
l
cd ../
ls
git stauts
git status
git add autophagy_codes/01_expr/03_h_coca.R autophagy_codes/01_expr/03_h_coca_cc.R autophagy_codes/06_methylation/03_methy_a_expr.R
git commit -m 'meth and coca_cc'
git push origin master
ls
ll
ls
ll
ls
cd autophagy_codes/
ls
ll
ll autophagy_codes/
cd autophagy_codes/
l
git status
git add -A
ll
cd autophagy_codes/
l
git status
git add -A
git status
git commit -m "gsea"
git push origin master
git status
l
cd /home/cliu18/liucj/projects/6.autophagy/
ls
cd autophagy_codes/
l
cd autophagy_codes/
l
git status
git add
git add -A
git status
git commit -m "gsva gsea"
git push origin master
ls
ll
l
cd expr_matrix/
l
rm expr_matrix/
l
ll
cd goodRCode/
l
ll
cd testCode/
l
ll
l
cd ../
ls
ll
cd autophagy_codes/
l
git status
ll autophagy_codes/11_cancer_stem_cell/
git add -A 
git commit -m "delete consensus matrix and update stem cel"
git push origin master
ps xf
l
top
l
cd liucj
cd
git status
git add -A
git commit -m 'gsva'
git push origin master
ll
ls
ps xf
liucj
find . -name .Rprofile
cd  "/extraspace/liucj/projects/4.SNORic/database"
ls
git status
git add -A
git commit -m "05_stemness"
git push origin master
top
ll
top
l
git status
git add -A
git commit -m "stemness"
git push origin master
ps xf
top
cd autophagy_codes/
ls
git status
git push -m "new gene list category"
git add -A
git push -m "new gene list category"
git commit  -m "new gene list category"
git push origin master
ll
l
cd autophagy_codes/
l
git status
git commit -m "gene expr"
git add A
git add -A
git commit -m "summary"
git push origin master
ll
git status
l
cd ../
ls
cd autophagy_codes/
l
find . -name "*R"
find . -name "*R"|xargs grep cowplot
find . -name "*R"|xargs 
find . -name "*R"|xargs grep cowplot
find . -name "*R"|xargs grep library
find . -name "*R"|xargs grep cowplot
ls
git status
git add -A
git commit -m "gsva other pathway"
git push origin master
ps xf
ll
liucj
ls
git status
git add -A
git commit -m "gsva other pathway"
git push origin master
ls
ps xf
top
ps xf
ps xf|awk '$3=="R"'
git status
git commit -m "gsva othter pathway"
git add -A
git commit -m "gsva othter pathway"
git push origin master
ll
liucj
git status
git add -A
git commit -m "gsva other pahtway"
git push origin master
git status
cd /extraspace/liucj/projects/6.autophagy/03_cnv/mutual_exclusive
ls
cd autophagy_codes/
ls
cd ../
git status
git add -A
git commit -m 'try error'
git push origin master
cd
ls
ll
cd autophagy_codes/
l
git add -A
git commit -m "mv to afh vs afl"
git push origin master
git add -A
git commit -m "mv to afh vs afl"
git push origin master
l
cd autophagy_codes/
ls
c dau
ls
cd autophagy_codes/
ls
ll
cd autophagy_codes/
l
git status
git add -A
git commit -m "afhl"
git push origin master
l
cd ./
l
cd ../
ls
ll
cd autophagy_codes/
l
cd ../
ls
cd autophagy_codes/
l
git status 
git add -A
git commit -m "new other pathway"
git push origin master
git push -f origin master
ll autophagy_codes/01_expr/nohup.out
git status
ll
du -sh *
cd mutationInPromoter
l
ls
cd ../
ls
la
cd autophagy_codes/
git status
git add -A
git commit -m "rm ftpconfig"
git push origin master
l
cd autophagy_codes/
ls
git status
git add -A
git commit -m "afhl"
git push origin master
ftp ftp://ftp.ccb.jhu.edu/pub/
lftp ftp://ftp.ccb.jhu.edu/pub/
gitr
ls
find . -name "*.R"
ps xf
top
ps xf
find . -name "*.R"
find . -name "*.R" -type f
ll
find .  -type f
find .  -type f -name "*R"
find .  -type f -name "*R"|grep -i rlang
find .  -type f -name "*R"|xargs grep -i rlang
find .  -type f -name "*R"|xargs grep -i cor.test
find .  -type f -name "*R"|xargs grep -i scale_color_gradient2
les ./autophagy_codes/01_expr/03_a_gene_expr.R
find .  -type f -name "*R"|xargs grep -i ratio
git status
git add -A
git commit -m 'afhl;
git commit -m 'afhl'
git push origin master
git status
git add -A
git commit -m 'afhl'
git push origin master
l
find .  -type f -name "*R"|xargs grep -i expand
les ./autophagy_codes/04_ccle/02_ccle_a_drug.R
find .  -type f -name "*R"|xargs grep -i hazard
les ./autophagy_codes/11_cancer_stem_cell/05_stemness_analysis.R
find .  -type f -name "*R"|xargs grep -i survminer
les ./autophagy_codes/12_merge_summary/02_expr_gsva_score.R
find .  -type f -name "*R"|xargs grep -i kmp
les ./autophagy_codes/11_cancer_stem_cell/05_stemness_analysis.R
find .  -type f -name "*R"|xargs grep -i "gridExtra::arrangeGrob"
les ./autophagy_codes/13_afh_vs_afl/01_af_h_l_classification.R
ls
cd autophagy_codes/
l
ll
cd autophagy_codes/
l
ll
cd testCode/
l
ll
cd autophagy_codes/
l
ll
cd testCode/
l
cd autophagy_codes/
l
vim .gitignore 
ll
git status
ggit add -A
git add -A
git commit -m "clinical" 
git push origin master
ll
cd autophagy_codes/
ls
cd autophagy_codes/
l
cd autophagy_codes/
ls
git status
git add -A
git commit -m "proensity score"
git push origin master
ps xf
kill -9 30865
ps xf
kill -9 30865
cd
ls
cd autophagy_codes/
l
cat RstudioWithGit.Rproj 
ls -al 
cd .Rproj.user/
ls
ll
l
la
cd .Rproj.user/
ls
cd autophagy_codes/
l
cd ../
ls
cd autophagy_codes/
l
ls
cd autophagy_codes/
ls
ll
rm fig_02_lm_rppa_p62_becn1.pdf 
l
ll
rm CESC_mRNAseq_samples.txt 
l
ll
cd ../
ls
ll
la
vim .gitignore 
ls
ll
ls
ll
ps 
ps xf
l
ls
cd