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<code>
export PYTHONPATH=""

unset PERL5LIB

export PATH=/TJPROJ2/GB/PUBLIC/software/GB_TR/mRNA/miniconda3/envs/immuno/bin:$PATH

mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate

python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/modify_couny.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/gene_fpkm.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls

Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/estimate.R --fpkm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls --outdir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate --condition /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/condition.xls --sample Sham_1,Sham_2,Sham_3,IRI_1,IRI_2,IRI_3,TA_1,TA_2,TA_3

/TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate

mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell

Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/Xcell.R --fpkm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls --outdir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell

python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/modify_xCell_RNAseq.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xcell_all.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xcell_select.xls

Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/bar_for_Xcell.R /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell

/TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell

mkdir -p /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram

cd /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram

python /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/count_TPM.py /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Quant/gene_count.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram/log2tpm.xls

Rscript /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/Immuno/IPS.R  /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram/log2tpm.xls /TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/pipline1.1/bin/Immuno/Immunophenogram-master/IPS_genes.txt

rm /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/gene_fpkm_name.xls /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate/fpkm.gct /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/1.Estimate/fpkm_out.gct /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/2.X_cell/xCell_interval.xls

/TJPROJ2/GB/PUBLIC/source/GB_TR/mRNA/gb_trans/gb_MedRef_man_pipline/bin/pdf_to_png --indir /TJPROJ6/NC_BG_SH/shouhou/202302/X101SC23010971-Z01-F001_reanalysis/test/Immuno/3.Immunophenogram
</code>

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