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MakeGencodeTSS @ 00ff3b14
bigWig @ d25a16e4
dREG @ 7ea59e30
dREG-Model @ 8d98b2e9
.gitmodules
ChIP.Rmd
E-MTAB-1086.sdrf.txt
ES_D0_H3K27ac_filtered_peaks.bed
ES_D10_H3K27ac_filtered_peaks.bed
ES_D2_H3K27ac_filtered_peaks.bed
ES_D5_H3K27ac_filtered_peaks.bed
ES_D7_H3K27ac_filtered_peaks.bed
GRO_seq_tunning.xlsx
H3K27ac_distribution.png
H3K27ac_filtered_peaks.bed
H3K27ac_filtered_peaks.tsv
H3K4me1_filtered_peaks.bed
H3K4me1_filtered_peaks.tsv
H3K4me3_3kb_flanking.bed
H3K4me3_distribution.png
H3K4me3_filtered_peaks.bed
H3K4me3_filtered_peaks.tsv
PMID_25842977_SraRunInfo.csv
README.md
Rna-seq_star.sh
SSP_filtered_peaks.bed
SSP_filtered_peaks.tsv
SSP_filtered_peaks_merged.bed
SUMMARY.xlsx
SUNP_filtered_peaks.bed
SUNP_filtered_peaks.tsv
call-peaks-macs-single.sh
call-transcripts-timecourse-norep.R
call-transcripts-timecourse-norep.sh
call-transcripts.R
call-transcripts.sh
cutoff_analysis.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
gencode.v19.annotation_capped_sites.bed
gencode_tss_3kb_flanking.bed
gene-counts.sh
genomewideCorrs_above0.7_promoterPlusMinus500kb_withGeneNames_32celltypeCategories.bed8
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
make-normal-signal.sh
merge_final-transcripts.bed
promoter_enhancer_processing.sh
rpkm.py
rpkm_gro.py
rpkm_name.py
short_short_paired.bed
short_short_paired_1kb.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