Vignette document

The analysis code is organized in a vignette document that you can download by following the link below.

file_name Link
ES_NS_Loops.html ES_NS_Loops.html
functions.R functions.R

Data files

The input data (and some of the output data) referred to in the
analysis code can be downloaded by following the links below.

file_name Link
afb.RData afb.RData
allChroms_Musm.txt allChroms_Musm.txt
AllTSS_NCBIM37_67_all_TSS_TTS.RData AllTSS_NCBIM37_67_all_TSS_TTS.RData
AP_profiles_CTCF_Rad21.RData AP_profiles_CTCF_Rad21.RData
cerebellum.specific.enhancer cerebellum.specific.enhancer
ES_chr10_binary.txt ES_chr10_binary.txt
ES_chr11_binary.txt ES_chr11_binary.txt
ES_chr12_binary.txt ES_chr12_binary.txt
ES_chr13_binary.txt ES_chr13_binary.txt
ES_chr14_binary.txt ES_chr14_binary.txt
ES_chr15_binary.txt ES_chr15_binary.txt
ES_chr16_binary.txt ES_chr16_binary.txt
ES_chr17_binary.txt ES_chr17_binary.txt
ES_chr18_binary.txt ES_chr18_binary.txt
ES_chr19_binary.txt ES_chr19_binary.txt
ES_chr1_binary.txt ES_chr1_binary.txt
ES_chr2_binary.txt ES_chr2_binary.txt
ES_chr3_binary.txt ES_chr3_binary.txt
ES_chr4_binary.txt ES_chr4_binary.txt
ES_chr5_binary.txt ES_chr5_binary.txt
ES_chr6_binary.txt ES_chr6_binary.txt
ES_chr7_binary.txt ES_chr7_binary.txt
ES_chr8_binary.txt ES_chr8_binary.txt
ES_chr9_binary.txt ES_chr9_binary.txt
ES_chrM_binary.txt ES_chrM_binary.txt
ES_chrX_binary.txt ES_chrX_binary.txt
ES_chrY_binary.txt ES_chrY_binary.txt
NS_chr10_binary.txt NS_chr10_binary.txt
NS_chr11_binary.txt NS_chr11_binary.txt
NS_chr12_binary.txt NS_chr12_binary.txt
NS_chr13_binary.txt NS_chr13_binary.txt
NS_chr14_binary.txt NS_chr14_binary.txt
NS_chr15_binary.txt NS_chr15_binary.txt
NS_chr16_binary.txt NS_chr16_binary.txt
NS_chr17_binary.txt NS_chr17_binary.txt
NS_chr18_binary.txt NS_chr18_binary.txt
NS_chr19_binary.txt NS_chr19_binary.txt
NS_chr1_binary.txt NS_chr1_binary.txt
NS_chr2_binary.txt NS_chr2_binary.txt
NS_chr3_binary.txt NS_chr3_binary.txt
NS_chr4_binary.txt NS_chr4_binary.txt
NS_chr5_binary.txt NS_chr5_binary.txt
NS_chr6_binary.txt NS_chr6_binary.txt
NS_chr7_binary.txt NS_chr7_binary.txt
NS_chr8_binary.txt NS_chr8_binary.txt
NS_chr9_binary.txt NS_chr9_binary.txt
NS_chrM_binary.txt NS_chrM_binary.txt
NS_chrX_binary.txt NS_chrX_binary.txt
NS_chrY_binary.txt NS_chrY_binary.txt
Compartment_tracks_50kb.RData Compartment_tracks_50kb.RData
Comp_tracks_ES_NS.RData Comp_tracks_ES_NS.RData
cor_matrices_50kb_PCA_IS.RData cor_matrices_50kb_PCA_IS.RData
cor_matrices_50kb.RData cor_matrices_50kb.RData
cortex.specific.enhancer cortex.specific.enhancer
CTCF_AP.RData CTCF_AP.RData
CTCF_Rad21_levels_per_cell_type.RData CTCF_Rad21_levels_per_cell_type.RData
CTCF_reads_extended_xx.RData CTCF_reads_extended_xx.RData
DI_10kb_ES_NS_in_situ.RData DI_10kb_ES_NS_in_situ.RData
domain_boundaries_IS.RData domain_boundaries_IS.RData
E14.5-brain.specific.enhancer E14.5-brain.specific.enhancer
ES1_counts_reverse.txt ES1_counts_reverse.txt
ES_25000_blocks.txt ES_25000_blocks.txt
ES2_counts_reverse.txt ES2_counts_reverse.txt
esc_IPF_pooled_5kb.hic esc_IPF_pooled_5kb.hic
esc_IPF_tcc_10kb.hic esc_IPF_tcc_10kb.hic
ES_comp1_50kb.bw ES_comp1_50kb.bw
ES_comp2_50kb.bw ES_comp2_50kb.bw
ES_comp3_50kb.bw ES_comp3_50kb.bw
esc.tcc.juicer.txt esc.tcc.juicer.txt
ES_FBS_CTCF_peaks.bed ES_FBS_CTCF_peaks.bed
ES_FBS_CTCF_summits.bed ES_FBS_CTCF_summits.bed
ES_FBS_Rad21_peaks.bed ES_FBS_Rad21_peaks.bed
ES_loops.txt ES_loops.txt
expr4binES.RData expr4binES.RData
expr4binNS.RData expr4binNS.RData
FBS_NS_all_peaks_CTCF_Rad21_counts.RData FBS_NS_all_peaks_CTCF_Rad21_counts.RData
induced_at_anchors_DAVID.txt induced_at_anchors_DAVID.txt
induced.genes.anchors.txt induced.genes.anchors.txt
induced.genes.inside2.txt induced.genes.inside2.txt
induced_inside_loops_DAVID.txt induced_inside_loops_DAVID.txt
induced_loops_ES_NS_CTCF_motif_ori.RData induced_loops_ES_NS_CTCF_motif_ori.RData
In_situ_ES_NS_DESeq_loop_comparision In_situ_ES_NS_DESeq_loop_comparision
InSitu_ES_pooled_10kb_my_object.RData InSitu_ES_pooled_10kb_my_object.RData
InSitu_ES_pooled_5kb_my_object.RData InSitu_ES_pooled_5kb_my_object.RData
InSitu_ES_pooled_5kb_my_object_repl_sep.RData InSitu_ES_pooled_5kb_my_object_repl_sep.RData
ES1_inter30.hic ES1_inter30.hic
ES2_inter30.hic ES2_inter30.hic
ES_inter30.hic ES_inter30.hic
ES_inter.hic ES_inter.hic
NS1_inter30.hic NS1_inter30.hic
NS2_inter30.hic NS2_inter30.hic
NS_inter30.hic NS_inter30.hic
NS_inter.hic NS_inter.hic
in_situ_loops_controls_ES_NS.RData in_situ_loops_controls_ES_NS.RData
In_situ_loops_merged_ES_NS_signal.RData In_situ_loops_merged_ES_NS_signal.RData
InSitu_NS_pooled_10kb_my_object.RData InSitu_NS_pooled_10kb_my_object.RData
InSitu_NS_pooled_5kb_my_object.RData InSitu_NS_pooled_5kb_my_object.RData
InSitu_NS_pooled_5kb_my_object_repl_sep.RData InSitu_NS_pooled_5kb_my_object_repl_sep.RData
intrachromosomal_10kb_IPF_ES_pooled.RData intrachromosomal_10kb_IPF_ES_pooled.RData
intrachromosomal_10kb_IPF_ES_repl_sep.RData intrachromosomal_10kb_IPF_ES_repl_sep.RData
intrachromosomal_50kb_IPF.RData intrachromosomal_50kb_IPF.RData
intrachromosomal_5kb_IPF_ES.RData intrachromosomal_5kb_IPF_ES.RData
intrachromosomal_5kb_IPF_ES_repl_sep.RData intrachromosomal_5kb_IPF_ES_repl_sep.RData
intrachromosomal_5kb_IPF_NS.RData intrachromosomal_5kb_IPF_NS.RData
intrachromosomal_5kb_IPF_NS_repl_sep.RData intrachromosomal_5kb_IPF_NS_repl_sep.RData
IS_dynamics_ES.RData IS_dynamics_ES.RData
IS_dynamics_NS.RData IS_dynamics_NS.RData
IS_loop_no_loop.RData IS_loop_no_loop.RData
LFMs_in_situ_5kb.RData LFMs_in_situ_5kb.RData
loop_compartment_domains.RData loop_compartment_domains.RData
loops_comparison_ti_EpiSC.RData loops_comparison_ti_EpiSC.RData
loops_comparison_ti_ns.RData loops_comparison_ti_ns.RData
loops_controls_ES_2i_NS.RData loops_controls_ES_2i_NS.RData
loops_controls_ES_NS.RData loops_controls_ES_NS.RData
Loops_coordinates.RData Loops_coordinates.RData
loops_ES_NS_clustered_for_comparison.RData loops_ES_NS_clustered_for_comparison.RData
Loops_merged_2i_NS.RData Loops_merged_2i_NS.RData
mESC_H3K27ac_peaks.bed mESC_H3K27ac_peaks.bed
mESC_H3K4me1_peaks.bed mESC_H3K4me1_peaks.bed
mESC_H3K4me3_peaks.bed mESC_H3K4me3_peaks.bed
mGA_repl_merged.RData mGA_repl_merged.RData
mGA_repl_sep.RData mGA_repl_sep.RData
mm9_CTCF_core_motif.bed mm9_CTCF_core_motif.bed
mm9_mappability_10kb_bins.RData mm9_mappability_10kb_bins.RData
mNSC_H3K27ac_peaks.bed mNSC_H3K27ac_peaks.bed
mNSC_H3K4me1_peaks.bed mNSC_H3K4me1_peaks.bed
mNSC_H3K4me3_peaks.bed mNSC_H3K4me3_peaks.bed
Mus_musculus.NCBIM37.67.gtf Mus_musculus.NCBIM37.67.gtf
NS1_counts_reverse.txt NS1_counts_reverse.txt
NS_25000_blocks.txt NS_25000_blocks.txt
NS2_counts_reverse.txt NS2_counts_reverse.txt
nsc_IPF_pooled_5kb.hic nsc_IPF_pooled_5kb.hic
nsc_IPF_tcc_10kb.hic nsc_IPF_tcc_10kb.hic
NS_comp1_50kb.bw NS_comp1_50kb.bw
NS_comp2_50kb.bw NS_comp2_50kb.bw
NS_comp3_50kb.bw NS_comp3_50kb.bw
nsc.tcc.juicer.txt nsc.tcc.juicer.txt
NS_CTCF_peaks.bed NS_CTCF_peaks.bed
NS_CTCF_summits.bed NS_CTCF_summits.bed
NS_loops.txt NS_loops.txt
NS_Rad21_peaks.bed NS_Rad21_peaks.bed
ordinary_versus_loop_domains_interactions.RData ordinary_versus_loop_domains_interactions.RData
PEI_and_loop_induction_intraDomain.RData PEI_and_loop_induction_intraDomain.RData
Rad21_AP.RData Rad21_AP.RData
Rad21_reads_extended_xx.RData Rad21_reads_extended_xx.RData
random_loops.RData random_loops.RData
repressed.genes.inside2.txt repressed.genes.inside2.txt
RNASeq_ESC_NSC.RData RNASeq_ESC_NSC.RData
si.RData si.RData
TCC_2i_cells_interactions.RData TCC_2i_cells_interactions.RData
TCC_2i_loops.RData TCC_2i_loops.RData
TCC_ES_NS_DESeq_loop_comparision TCC_ES_NS_DESeq_loop_comparision
TCC_ES_NS_interactions.RData TCC_ES_NS_interactions.RData
TCC_ES_NS_loops.RData TCC_ES_NS_loops.RData
TCC_IPF_10kb_ES_NS_pooled.RData TCC_IPF_10kb_ES_NS_pooled.RData
TCC_IPF_10kb_ES_NS_repl_sep.RData TCC_IPF_10kb_ES_NS_repl_sep.RData
TCC_IPF_10kbMatrices_pooled_EpiSC.RData TCC_IPF_10kbMatrices_pooled_EpiSC.RData
TCC_IPF_10kbMatrices_repl_sep_EpiSC.RData TCC_IPF_10kbMatrices_repl_sep_EpiSC.RData
TCC_IPF_10kb_pooled_ES_2i.RData TCC_IPF_10kb_pooled_ES_2i.RData
TCC_IPF_10kb_repl_sep_ES_2i.RData TCC_IPF_10kb_repl_sep_ES_2i.RData
TCC_LFMs_10_kb_2i.RData TCC_LFMs_10_kb_2i.RData
TCC_LFMs_10_kb_Epi.RData TCC_LFMs_10_kb_Epi.RData
TCC_LFMs_10_kb.RData TCC_LFMs_10_kb.RData
TCC_Loops_merged_ES_NS.RData TCC_Loops_merged_ES_NS.RData
Ti_versus_EpiSC_APA.RData Ti_versus_EpiSC_APA.RData
vsnNormalizedSetAllsamples.RData vsnNormalizedSetAllsamples.RData