LICENSE
MANIFEST.in
README.md
conv_clipping.sh
get_gene_length.py
run_RNAseqpipe.py
setup.py
./NOISeq.py
./RNAseqpip.py
./__init__.py
./_version.py
./conv_clipping.sh
./cptDE.py
./cufflinks.py
./expression_filter.py
./func.py
./get_gene_length.py
./get_geneids.py
./gtf_cuff_table.py
./hisat.py
./htseq.py
./progsuit.py
./run_RNAseqpipe.py
./seq2exp.py
./stringtie.py
./verse.py
./confs/QC.conf
./confs/RNApip_lnc.conf
./confs/base.back
./confs/base.conf
./confs/base.template
./confs/dUTP.conf
./confs/fr_firststrand.conf
./confs/fr_secondstrand.conf
./confs/gc.conf
./confs/gc_no_gff.conf
./confs/hisat_cuff_verse.conf
./confs/hisat_htseq_count.conf
./confs/hisat_stringtie_verse.conf
./confs/hisat_verse_count.conf
./confs/hs38.conf
./confs/mRNA.conf
./confs/mm38.conf
./confs/test_gc.conf
./confs/test_gc_no_gff.conf
./confs/unstrand.conf
./confs/zf.conf
./confs/zf11.conf
./expression/__init__.py
./expression/count_merge.py
./expression/normalize.R
./expression/normalize.py
./expression/salmon_quantify.py
./expression/salmon_quantify.sh
./funcAnnot/__init__.py
./funcAnnot/annot_from_db.py
./funcAnnot/find_genes_in_genome.py
./funcAnnot/subset_fasta.py
./funcAnnot/b2gprog/GOannot.py
./funcAnnot/b2gprog/__init__.py
./funcAnnot/b2gprog/format_godb.R
./funcAnnot/b2gprog/gostat_goplot_RamiGO_in.R
./funcAnnot/b2gprog/gostat_goplot_RamiGO_out.R
./funcAnnot/b2gprog/gostats.R
./funcAnnot/b2gprog/tmp.R
./funcAnnot/blast2go/blast2go.sh
./funcAnnot/go/enrich_bubble.R
./funcAnnot/go/goplot.R
./funcAnnot/kegg/KOannot.py
./funcAnnot/kegg/__init__.py
./funcAnnot/kegg/annot2go_stat.py
./funcAnnot/kegg/kaas_online.py
./funcAnnot/kegg/kegg_annot2mapper.py
./funcAnnot/kegg/heatmap/cmd.sh
./funcAnnot/kegg/heatmap/heatmap.R
./funcAnnot/kegg/heatmap/heatmap.sh
./funcAnnot/kegg/heatmap/trace_exp.sh
./funcAnnot/kegg/koenrich/__init__.py
./funcAnnot/kegg/koenrich/keggCountal.py
./funcAnnot/kegg/koenrich/keggenrich.py
./funcAnnot/kegg/koenrich/keggenrich.sh
./funcAnnot/kegg/koenrich/mykeggenrich.R
./funcAnnot/kegg/map_NOIout_pip/example.sh
./group_data/group_data.txt
./group_data/group_data_temp.txt
./group_data/l_group_data.txt
./group_data/m_group_data.txt
./group_data/test_group_data.txt
./install/__init__.py
./install/copy_conf.py
./install/copy_test.py
./install/init_base_conf.py
./install/install.py
./stat/mapping_rate_estimate.sh
./test/__init__.py
./test/__init__.pyc
./test/function_for_test.py
./test/test_FuncAnnot.py
./test/test_Pipe.py
./test/test_QC.py
./test/test_tools.py
./test/RNAseqpip_data/cmd
./test/RNAseqpip_data/init_test_conf.sh
./test/RNAseqpip_data/init_test_data.sh
./test/RNAseqpip_data/knownbugs
./test/RNAseqpip_data/run_test.sh
./test/RNAseqpip_data/run_test_old.sh
./test/RNAseqpip_data/testcmd.txt
./test/RNAseqpip_data/data/merged.fa
./test/RNAseqpip_data/data/test.dlmrna.gc.final.gff
./test/RNAseqpip_data/data/test.dlmrna.gc.final.gtf
./test/RNAseqpip_data/data/test_GO_enrich.txt
./test/RNAseqpip_data/data/test_genome.fa
./test/RNAseqpip_data/data/test_genome.fa.fai
./test/RNAseqpip_data/data/test_genome_idx.1.ht2
./test/RNAseqpip_data/data/test_genome_idx.2.ht2
./test/RNAseqpip_data/data/test_genome_idx.3.ht2
./test/RNAseqpip_data/data/test_genome_idx.4.ht2
./test/RNAseqpip_data/data/test_genome_idx.5.ht2
./test/RNAseqpip_data/data/test_genome_idx.6.ht2
./test/RNAseqpip_data/data/test_genome_idx.7.ht2
./test/RNAseqpip_data/data/test_genome_idx.8.ht2
./test/RNAseqpip_data/data/test_human.gtf
./test/RNAseqpip_data/data/confs/gc.conf
./test/RNAseqpip_data/data/confs/gc_no_gff.conf
./test/RNAseqpip_data/data/confs/gc_no_gff_template.conf
./test/RNAseqpip_data/data/confs/gc_template.conf
./test/RNAseqpip_data/data/fqs/test1_1.fq
./test/RNAseqpip_data/data/fqs/test1_2.fq
./test/RNAseqpip_data/data/fqs/test2_1.fq
./test/RNAseqpip_data/data/fqs/test2_2.fq
./test/RNAseqpip_data/data/fqs/test3_1.fq
./test/RNAseqpip_data/data/fqs/test3_2.fq
./test/RNAseqpip_data/data/gps/big_group_data.txt
./test/RNAseqpip_data/data/gps/small_group_data.txt
./test/RNAseqpip_data/data/gps/small_group_data_template.txt
./test/RNAseqpip_data/data/salmon_index/complete_ref_lens.bin
./test/RNAseqpip_data/data/salmon_index/ctable.bin
./test/RNAseqpip_data/data/salmon_index/ctg_offsets.bin
./test/RNAseqpip_data/data/salmon_index/duplicate_clusters.tsv
./test/RNAseqpip_data/data/salmon_index/info.json
./test/RNAseqpip_data/data/salmon_index/mphf.bin
./test/RNAseqpip_data/data/salmon_index/pos.bin
./test/RNAseqpip_data/data/salmon_index/pre_indexing.log
./test/RNAseqpip_data/data/salmon_index/rank.bin
./test/RNAseqpip_data/data/salmon_index/refAccumLengths.bin
./test/RNAseqpip_data/data/salmon_index/ref_indexing.log
./test/RNAseqpip_data/data/salmon_index/reflengths.bin
./test/RNAseqpip_data/data/salmon_index/refseq.bin
./test/RNAseqpip_data/data/salmon_index/seq.bin
./test/RNAseqpip_data/data/salmon_index/versionInfo.json
./test/RNAseqpip_data/module_test/test_blast2go.sh
./test/RNAseqpip_data/module_test/data/test.fa
./test/RNAseqpip_data/module_test/data/test.gtf
./test/RNAseqpip_data/module_test/data/test1.fa
./test/RNAseqpip_data/module_test/data/test_noi.fasta
./test/RNAseqpip_data/module_test/data/test_noi.out
./test/RNAseqpip_data/module_test/test_out/final.annot
./test/RNAseqpip_data/module_test/test_out/tmp0.xml
./test/RNAseqpip_data/module_test/test_out/tmp1.xml
./test/RNAseqpip_data/module_test/test_out/tmp_fa0.xml
./test/RNAseqpip_data/module_test/test_out/tmp_fa1.xml
./test/RNAseqpip_data/refout/hv_out/TEST1/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hv_out/TEST1/sort.exon.txt
./test/RNAseqpip_data/refout/hv_out/TEST2/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hv_out/TEST2/sort.exon.txt
./test/RNAseqpip_data/refout/hv_out/TEST3/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hv_out/TEST3/sort.exon.txt
./test/RNAseqpip_data/refout/hv_out/TEST4/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hv_out/TEST4/sort.exon.txt
./test/RNAseqpip_data/refout/hv_out/salmon/quant_merge.elen
./test/RNAseqpip_data/refout/hv_out/salmon/quant_merge.len
./test/RNAseqpip_data/refout/hv_out/salmon/quant_merge.numreads
./test/RNAseqpip_data/refout/hv_out/salmon/quant_merge.tpm
./test/RNAseqpip_data/refout/hvc_count_out/all_flagstat.txt
./test/RNAseqpip_data/refout/hvc_count_out/merged.count
./test/RNAseqpip_data/refout/hvc_count_out/TEST1/flagstat.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST1/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST1/sort.exon.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST1/transcripts.gtf
./test/RNAseqpip_data/refout/hvc_count_out/TEST2/flagstat.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST2/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST2/sort.exon.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST2/transcripts.gtf
./test/RNAseqpip_data/refout/hvc_count_out/TEST3/flagstat.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST3/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST3/sort.exon.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST3/transcripts.gtf
./test/RNAseqpip_data/refout/hvc_count_out/TEST4/flagstat.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST4/sort.exon.summary.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST4/sort.exon.txt
./test/RNAseqpip_data/refout/hvc_count_out/TEST4/transcripts.gtf
./test/RNAseqpip_data/refout/hvc_count_out/merged_asm/merged.fa
./test/RNAseqpip_data/refout/hvc_count_out/merged_asm/merged.gtf
./test/RNAseqpip_data/refout/hvc_count_out/salmon/quant_merge.elen
./test/RNAseqpip_data/refout/hvc_count_out/salmon/quant_merge.len
./test/RNAseqpip_data/refout/hvc_count_out/salmon/quant_merge.numreads
./test/RNAseqpip_data/refout/hvc_count_out/salmon/quant_merge.tpm
./test/RNAseqpip_data/refout/salmon/quant_merge.elen
./test/RNAseqpip_data/refout/salmon/quant_merge.len
./test/RNAseqpip_data/refout/salmon/quant_merge.numreads
./test/RNAseqpip_data/refout/salmon/quant_merge.tpm
./test/RNAseqpip_data/refout/tools/test_get_gene_length_gc.txt
./test/RNAseqpip_data/refout/tools/test_get_gene_length_hs.txt
./test/RNAseqpip_data/refout/tools/test_get_gene_length_hs_fn.txt
./test/RNAseqpip_data/refout/tools/test_get_gene_length_hs_tx.txt
./test/__pycache__/__init__.cpython-310.pyc
./test/__pycache__/__init__.cpython-38.pyc
./test/__pycache__/function_for_test.cpython-27-PYTEST.pyc
./test/__pycache__/function_for_test.cpython-310-pytest-7.1.2.pyc
./test/__pycache__/function_for_test.cpython-38-pytest-6.2.5.pyc
./test/__pycache__/test_FuncAnnot.cpython-27-PYTEST.pyc
./test/__pycache__/test_FuncAnnot.cpython-310-pytest-7.1.2.pyc
./test/__pycache__/test_FuncAnnot.cpython-38-pytest-6.2.5.pyc
./test/__pycache__/test_Pipe.cpython-27-PYTEST.pyc
./test/__pycache__/test_Pipe.cpython-310-pytest-7.1.2.pyc
./test/__pycache__/test_Pipe.cpython-38-pytest-6.2.5.pyc
./test/__pycache__/test_QC.cpython-310-pytest-7.1.2.pyc
./test/__pycache__/test_QC.cpython-38-pytest-6.2.5.pyc
./test/__pycache__/test_tools.cpython-310-pytest-7.1.2.pyc
./test/__pycache__/test_tools.cpython-38-pytest-6.2.5.pyc
RNAseqpipe.egg-info/PKG-INFO
RNAseqpipe.egg-info/SOURCES.txt
RNAseqpipe.egg-info/dependency_links.txt
RNAseqpipe.egg-info/requires.txt
RNAseqpipe.egg-info/top_level.txt
expression/count_merge
install/post_RNAseqpipe_install
stat/merge_flagstat.py
test/__init__.py
test/function_for_test.py
test/test_FuncAnnot.py
test/test_Pipe.py
test/test_QC.py
test/test_tools.py
test/RNAseqpip_data/init_test_conf.sh
test/RNAseqpip_data/init_test_data.sh
test/RNAseqpip_data/run_test.sh
test/RNAseqpip_data/run_test_old.sh
test/RNAseqpip_data/module_test/test_blast2go.sh