Scripts

Scripts for integrative analysis ChiP-Seq, RNA-Seq, WG-Seq and WE-Seq for TLX3 project

Name		Name	Last commit message	Last commit date
im		im
package		package
.Rhistory		.Rhistory
.gitignore		.gitignore
Browser_genes_view.py		Browser_genes_view.py
ChiPeakAnno.R		ChiPeakAnno.R
Class_test.py		Class_test.py
Closest_Genes.py		Closest_Genes.py
DEG_TLX3.py		DEG_TLX3.py
DUXBL_TLX3.py		DUXBL_TLX3.py
Density_mutation.py		Density_mutation.py
Draw_Signal_tracks.py		Draw_Signal_tracks.py
Enh_Genes_Tlx_peaks.ipynb		Enh_Genes_Tlx_peaks.ipynb
Enh_Mut_Manip.py		Enh_Mut_Manip.py
Enh_Tlx_peaks_Mutation.ipynb		Enh_Tlx_peaks_Mutation.ipynb
EnrichLib_Jupy.py		EnrichLib_Jupy.py
EnrichRLib.py		EnrichRLib.py
EnrichrLib_test.ipynb		EnrichrLib_test.ipynb
EnrichrLib_test01.py		EnrichrLib_test01.py
EnrichrLib_tutorial.ipynb		EnrichrLib_tutorial.ipynb
EnrichrLib_tutorial.py		EnrichrLib_tutorial.py
FANTOM_enhHMM_bed_manip.py		FANTOM_enhHMM_bed_manip.py
FANTOM_enhn_TALLsuppress_gene_analys.py		FANTOM_enhn_TALLsuppress_gene_analys.py
GeneEnrichTest.py		GeneEnrichTest.py
Genome_TLX3.ipynb		Genome_TLX3.ipynb
GseaPy_analysis.py		GseaPy_analysis.py
Gsea_express.ipynb		Gsea_express.ipynb
Gsea_express.py		Gsea_express.py
IMMport_gene_lists.py		IMMport_gene_lists.py
Kataegis.py		Kataegis.py
MGP_vcf_add_chr.py		MGP_vcf_add_chr.py
MSD_cacl.py		MSD_cacl.py
ORC2_bed_manip.py		ORC2_bed_manip.py
PRC2_bed_manip.py		PRC2_bed_manip.py
Pierre_gene_set_list.py		Pierre_gene_set_list.py
Plotty.ipynb		Plotty.ipynb
PyGenomeTrack_exmpl.py		PyGenomeTrack_exmpl.py
PyGenomeTrack_exmpl.pyc		PyGenomeTrack_exmpl.pyc
RAG_TLX3_peaks_analysis.py		RAG_TLX3_peaks_analysis.py
README.md		README.md
RNA_expression_processing.py		RNA_expression_processing.py
RNA_expression_processing.pyc		RNA_expression_processing.pyc
RNA_expression_processing_bck.py		RNA_expression_processing_bck.py
RPCalc.py		RPCalc.py
RP_TSS_3K.py		RP_TSS_3K.py
RP_TSS_3K_(TLX3-vs-RAG)_mm9.py		RP_TSS_3K_(TLX3-vs-RAG)_mm9.py
RP_Tlx3_bind.py		RP_Tlx3_bind.py
RP_manip.py		RP_manip.py
RP_mm10_mm9.py		RP_mm10_mm9.py
RXT_TLX3_signals.py		RXT_TLX3_signals.py
RegNetwork.py		RegNetwork.py
ScatterPlot_test.py		ScatterPlot_test.py
Snakefile		Snakefile
Snakefile_mm10		Snakefile_mm10
T-ALL_gmt.py		T-ALL_gmt.py
TCRa_TCRb_TLXvsRAG.py		TCRa_TCRb_TLXvsRAG.py
TLX3_Enhancers-RAG_2019.ipynb		TLX3_Enhancers-RAG_2019.ipynb
TLX3_Enhancers-TLX3_2019.ipynb		TLX3_Enhancers-TLX3_2019.ipynb
TLX3_Project_Story_2019-RAG.py		TLX3_Project_Story_2019-RAG.py
TLX3_Project_Story_2019.py		TLX3_Project_Story_2019.py
TLX3_Promoters_3K_RAG_2019.ipynb		TLX3_Promoters_3K_RAG_2019.ipynb
TLX3_Promoters_3K_TLX3_2019.ipynb		TLX3_Promoters_3K_TLX3_2019.ipynb
TLX3_Promoters_RAG_2019.ipynb		TLX3_Promoters_RAG_2019.ipynb
TLX3_Promoters_TLX3_2019.ipynb		TLX3_Promoters_TLX3_2019.ipynb
TLX3_RUNX_annot.R		TLX3_RUNX_annot.R
TLX3_peaks_analysis.py		TLX3_peaks_analysis.py
TLX3_peaks_annot.R		TLX3_peaks_annot.R
TLX3_peaks_annot.py		TLX3_peaks_annot.py
TLX3_peaks_annot2.py		TLX3_peaks_annot2.py
TLX3_peaks_motifs.py		TLX3_peaks_motifs.py
TLX3pk_Enh_TSS2Kb.py		TLX3pk_Enh_TSS2Kb.py
TLX3pk_Enh_TSS2Kb_gseapy.py		TLX3pk_Enh_TSS2Kb_gseapy.py
TLXRAGTAP-17_st16_annot.R		TLXRAGTAP-17_st16_annot.R
WES-Scikit-allel.ipynb		WES-Scikit-allel.ipynb
WGS-TLX3-scikit-allel.ipynb		WGS-TLX3-scikit-allel.ipynb
WGS-TLX3-scikit-allel.py		WGS-TLX3-scikit-allel.py
analys_ChiPseeker.ipynb		analys_ChiPseeker.ipynb
analys_ChiPseekerShortExplain.ipynb		analys_ChiPseekerShortExplain.ipynb
analys_DESeq2-Explain.ipynb		analys_DESeq2-Explain.ipynb
analys_DESeq2.ipynb		analys_DESeq2.ipynb
analys_DESeq2genes.r		analys_DESeq2genes.r
analysis_ChiPeakAnno.ipynb		analysis_ChiPeakAnno.ipynb
bdg2bw		bdg2bw
bigWigSummary		bigWigSummary
big_sammary_table.py		big_sammary_table.py
cluster.py		cluster.py
clusterBins_TF.py		clusterBins_TF.py
code_snippets.txt.sh		code_snippets.txt.sh
codes_from_metaseq.py		codes_from_metaseq.py
colored_teable.py		colored_teable.py
colors.py		colors.py
compare_tracks.py		compare_tracks.py
compare_tracks_all.ipynb		compare_tracks_all.ipynb
compare_tracks_all.py		compare_tracks_all.py
compare_tracks_inter.ipynb		compare_tracks_inter.ipynb
compare_tracks_inter.py		compare_tracks_inter.py
compare_tracks_inter02.py		compare_tracks_inter02.py
config.yaml		config.yaml
convert_svg2pdf.sh		convert_svg2pdf.sh
copy-TAP-data.py		copy-TAP-data.py

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