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Venkat Malladi
TFSEE
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Moved extra files.
Venkat Malladi
authored
5 years ago
3a4bb168
3a4bb168844d01746663bb941d42a6583f245444
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analysis_output
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analysis
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GRO_seq_TFSEE
Histone_TFSEE
gene_matrix
ChIP.Rmd
E-MTAB-1086.sdrf.txt
ES_D0_H3K27ac_filtered_peaks.bed
ES_D0_Histone_enhancers.bed
ES_D0_Histone_enhancers_1kb.bed
ES_D0_gro-seq_enhancers.bed
ES_D0_gro-seq_enhancers_1kb.bed
ES_D10_H3K27ac_filtered_peaks.bed
ES_D10_Histone_enhancers.bed
ES_D10_Histone_enhancers_1kb.bed
ES_D10_gro-seq_enhancers.bed
ES_D10_gro-seq_enhancers_1kb.bed
ES_D2_H3K27ac_filtered_peaks.bed
ES_D2_Histone_enhancers.bed
ES_D2_Histone_enhancers_1kb.bed
ES_D2_gro-seq_enhancers.bed
ES_D2_gro-seq_enhancers_1kb.bed
ES_D5_H3K27ac_filtered_peaks.bed
ES_D5_Histone_enhancers.bed
ES_D5_Histone_enhancers_1kb.bed
ES_D5_gro-seq_enhancers.bed
ES_D5_gro-seq_enhancers_1kb.bed
ES_D7_H3K27ac_filtered_peaks.bed
ES_D7_Histone_enhancers.bed
ES_D7_Histone_enhancers_1kb.bed
ES_D7_gro-seq_enhancers.bed
ES_D7_gro-seq_enhancers_1kb.bed
ES_Histone_universe_enhancers.tsv
GRO_seq_tunning.xlsx
GRO_seq_tunning_updated.xlsx
Gro_percentages.png
H3K27ac_all_filtered_peaks.bed
H3K27ac_all_filtered_peaks.tsv
H3K27ac_distribution.png
H3K27ac_filtered_peaks.bed
H3K27ac_filtered_peaks.tsv
H3K4me1_all_filtered_peaks.bed
H3K4me1_all_filtered_peaks.tsv
H3K4me1_distribution.png
H3K4me1_filtered_peaks.bed
H3K4me1_filtered_peaks.tsv
H3K4me3_3kb_flanking.bed
H3K4me3_all_filtered_peaks.bed
H3K4me3_all_filtered_peaks.tsv
H3K4me3_distribution.png
H3K4me3_filtered_peaks.bed
H3K4me3_filtered_peaks.tsv
Histone_h3k27ac_filtered_peaks.bed
Histone_h3k27ac_filtered_peaks.tsv
Histone_h3k4me1_filtered_peaks.bed
Histone_h3k4me1_filtered_peaks.tsv
Histone_pe_filtered_peaks.bed
Histone_pe_filtered_peaks.tsv
Histone_percentages.png
Histone_putative_enhancers.bed
PMID_25842977_SraRunInfo.csv
RNA_distribution.png
Rna-seq_star.sh
SSP_distribution.png
SSP_filtered_peaks.bed
SSP_filtered_peaks.tsv
SSP_filtered_peaks_merged.bed
SSP_filtered_peaks_sum.tsv
SSP_sum.tsv
SUNP_distribution.png
SUNP_filtered_peaks.bed
SUNP_filtered_peaks.tsv
SUNP_sum.tsv
VennDiagram.ipynb
biotypes.txt
call-peaks-macs-single.sh
call-transcripts-timecourse-norep.R
call-transcripts-timecourse-norep.sh
call-transcripts.R
call-transcripts.sh
cutoff_analysis.py
cutoff_analysis_gro.py
define_histone_window.py
define_short_transcripts.py
define_small_transcripts.py
enhancers_1kb.bed
enhancers_renamed.bed
enhancers_to_gene.bed
excluded_3kb_flanking.bed
excluded_regions_processing.sh
extend_histone_1kb.py
fpkm.py
gencode.v19.annotation.gtf
gencode.v19.annotation_capped_sites.bed
gencode.v19.annotation_protein_coding.gtf
gencode.v19.annotation_protein_coding_ids.txt
gencode_tss_3kb_flanking.bed
gene-counts.sh
genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8
gro-seq_enhancer_plots.py
gro-seq_list.csv
groseq_processing.sh
h3k27ac_list.csv
h3k27ac_processing.sh
h3k4me1_list.csv
h3k4me1_processing.sh
h3k4me3_list.csv
h3k4me3_processing.sh
hg19.chrom.sizes
histone_centered_processing.sh
histone_enhancer_plots.py
late_venn.eps
make-normal-signal.sh
merge_final-transcripts.bed
pre_venn.eps
promoter_enhancer_processing.sh
protein_coding_genes.txt
putative_enhancer_processing.sh
putative_histone_enhancers.csv
rna_list.csv
rnaseq_processing.sh
rpkm.py
rpkm_gro.py
rpkm_name.py
short_short_paired.bed
short_short_paired_1kb.bed
short_transcripts.bed
short_unpaired.bed
short_unpaired_1kb.bed
tune-hmm.R
tune-hmm.sh
universe_enhancer_H3K27ac.bed
universe_enhancer_H3K4me1.bed
universe_enhancer_transcripts.bed
