Scripts

Bash, awk, R, python scripts and executables for genomics and transcriptomics

Authors: Sarah Djebali, Alessandra Breschi, Sylvain Foissac

In order to clone the repository do

git clone https://github.com/sdjebali/Scripts.git

Name		Name	Last commit message	Last commit date
Latest commit History 198 Commits
old		old
palettes		palettes
save		save
waiting		waiting
2way_venn.sh		2way_venn.sh
3way_venn.sh		3way_venn.sh
4way_venn.sh		4way_venn.sh
GO_enrichment.R		GO_enrichment.R
GO_enrichment_FDR.R		GO_enrichment_FDR.R
LICENSE		LICENSE
README.md		README.md
Set3.12.txt		Set3.12.txt
TrtoEx_RPKM.sh		TrtoEx_RPKM.sh
TrtoGn_RPKM.sh		TrtoGn_RPKM.sh
add.bin.pairs.to.peak.pairs.awk		add.bin.pairs.to.peak.pairs.awk
add.hsgncoord.and.mmorthinfo.awk		add.hsgncoord.and.mmorthinfo.awk
add.info.to.vcf.awk		add.info.to.vcf.awk
add_2classes_feelnc_tr_gn_bt_to_tmerge.awk		add_2classes_feelnc_tr_gn_bt_to_tmerge.awk
add_3classes_feelnc_tr_gn_bt_to_smerge.awk		add_3classes_feelnc_tr_gn_bt_to_smerge.awk
add_4classes_feelnc_gnbt_to_ensagnost_tmerge.awk		add_4classes_feelnc_gnbt_to_ensagnost_tmerge.awk
add_5p_3p_extlist.awk		add_5p_3p_extlist.awk
add_codinginfo_about3ppartjunction.awk		add_codinginfo_about3ppartjunction.awk
add_codinginfo_about5ppartjunction.awk		add_codinginfo_about5ppartjunction.awk
add_double_quotes_to_gff.awk		add_double_quotes_to_gff.awk
add_gninfo_to_promtopromoverlap.awk		add_gninfo_to_promtopromoverlap.awk
add_intermclass_andgnlist.awk		add_intermclass_andgnlist.awk
add_maxbegend_to_chimjunc2.awk		add_maxbegend_to_chimjunc2.awk
add_novelty_status_to_tagada_file.awk		add_novelty_status_to_tagada_file.awk
add_overlap_info_to_junctions.sh		add_overlap_info_to_junctions.sh
add_quantile.R		add_quantile.R
add_sense_antisense_read_counts_to_segments_frombam.sh		add_sense_antisense_read_counts_to_segments_frombam.sh
add_utrs_to_gtffile.awk		add_utrs_to_gtffile.awk
allinfo_to_distrib.awk		allinfo_to_distrib.awk
analyse_transcript_models.sh		analyse_transcript_models.sh
annot_to_introns_with_ds_and_can.sh		annot_to_introns_with_ds_and_can.sh
atac.meta.2.atacseq.sheet.awk		atac.meta.2.atacseq.sheet.awk
atac.meta.2.ena.sheet.awk		atac.meta.2.ena.sheet.awk
atac.meta.2.faang.sheet.awk		atac.meta.2.faang.sheet.awk
atac.meta.2.run.sheet.awk		atac.meta.2.run.sheet.awk
atac.qc.techrep.2.biorep.awk		atac.qc.techrep.2.biorep.awk
atacataccorr.to.geneoftsspeak.with.peaknb.awk		atacataccorr.to.geneoftsspeak.with.peaknb.awk
atacnorm.to.oksampleforcorr.awk		atacnorm.to.oksampleforcorr.awk
atacqc.aggregate.techrepinfo.ofabiorep.awk		atacqc.aggregate.techrepinfo.ofabiorep.awk
atacsumstat2barplotinput1.awk		atacsumstat2barplotinput1.awk
atacsumstat2barplotinput2-2.awk		atacsumstat2barplotinput2-2.awk
atacsumstat2barplotinput2.awk		atacsumstat2barplotinput2.awk
atacsumstat2barplotinput3.awk		atacsumstat2barplotinput3.awk
barplot.specific.1.sh		barplot.specific.1.sh
bed2allformapeval.awk		bed2allformapeval.awk
bed2gff2.awk		bed2gff2.awk
bedpe.liftover.sh		bedpe.liftover.sh
bedpe.sumstats.sh		bedpe.sumstats.sh
benchmark_chimeric_junction.sh		benchmark_chimeric_junction.sh
bigclassif2codclassofposclass.awk		bigclassif2codclassofposclass.awk
boxplots.sh		boxplots.sh
cbbPalette.8.txt		cbbPalette.8.txt
check_simple.sh		check_simple.sh
chim_bedpe_to_don_acc_tsv.awk		chim_bedpe_to_don_acc_tsv.awk
chim_txt_to_bedpe.awk		chim_txt_to_bedpe.awk
chim_txt_to_gff_ssext.awk		chim_txt_to_gff_ssext.awk
chinput2onlybaitok.awk		chinput2onlybaitok.awk
chinputtech2biorep.awk		chinputtech2biorep.awk
class2simpleclass.awk		class2simpleclass.awk
clean_gtf_after2feelncruns.awk		clean_gtf_after2feelncruns.awk
compare_bam.sh		compare_bam.sh
compare_chim_junc.awk		compare_chim_junc.awk
compare_chimjunc_sv.R		compare_chimjunc_sv.R
compare_multiple_trsets_wrt_reftrset.sh		compare_multiple_trsets_wrt_reftrset.sh
compare_two_annot_at_exandgnlev.sh		compare_two_annot_at_exandgnlev.sh
compmerge		compmerge
comptr_to_nbtr_in_classes.awk		comptr_to_nbtr_in_classes.awk
compute.internalexlonger500bp.awk		compute.internalexlonger500bp.awk
compute.trandinternalex.longer500bp.sh		compute.trandinternalex.longer500bp.sh
compute_boundaries.awk		compute_boundaries.awk
compute_coverage_from_elements_gal_nocluster_better.sh		compute_coverage_from_elements_gal_nocluster_better.sh
compute_detected_tr_gn.sh		compute_detected_tr_gn.sh
compute_gene_rpkm_from_simple_counts.sh		compute_gene_rpkm_from_simple_counts.sh
compute_pearson_correlation_inlog_better.sh		compute_pearson_correlation_inlog_better.sh
compute_prop.awk		compute_prop.awk
compute_spearman_correlation.sh		compute_spearman_correlation.sh
compute_tp_from_refine_comptr_and_reflist.awk		compute_tp_from_refine_comptr_and_reflist.awk
compute_wilcox_test.sh		compute_wilcox_test.sh
concat_two_expr_matrices_long_small.awk		concat_two_expr_matrices_long_small.awk
conn2connwithnbsnps.awk		conn2connwithnbsnps.awk
conn2connwithsnplists.awk		conn2connwithsnplists.awk
conn2samegnpromelt2.awk		conn2samegnpromelt2.awk
conncompSV2vcf.awk		conncompSV2vcf.awk
conncompSV2vcf_better.awk		conncompSV2vcf_better.awk
connected_components.py		connected_components.py
connfilewithnbsnp2simplerstats.awk		connfilewithnbsnp2simplerstats.awk
cutgff.awk		cutgff.awk
decorate.conncomp.from.promelt2.awk		decorate.conncomp.from.promelt2.awk
detected_elements_sumstats.sh		detected_elements_sumstats.sh
divide_bam_file_into_chr.sh		divide_bam_file_into_chr.sh
divide_bam_file_into_chr_fast.sh		divide_bam_file_into_chr_fast.sh
divide_into_chr.sh		divide_into_chr.sh
divide_into_chr_zipped.sh		divide_into_chr_zipped.sh
divide_into_strand.sh		divide_into_strand.sh
duplseq		duplseq
edgeR.analysis.R		edgeR.analysis.R

License

sdjebali/Scripts

Folders and files

Latest commit

History