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Code and annotation files for MAP-C paper

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Rgt1_1-400_Jpred4
Rgt1_1-400_Jpred4
 
 
Rgt1_401-1170_Jpred4
Rgt1_401-1170_Jpred4
 
 
microarray
microarray
 
 
references
references
 
 
yetfasco
yetfasco
 
 
3bp_substitution.R
3bp_substitution.R
 
 
3bp_substitution.fa
3bp_substitution.fa
 
 
3bp_substitution.sh
3bp_substitution.sh
 
 
3bp_substitution_all.sh
3bp_substitution_all.sh
 
 
3bp_substitution_samples.txt
3bp_substitution_samples.txt
 
 
3bp_substitution_sequences.txt
3bp_substitution_sequences.txt
 
 
ChIPseq_RNA_comparison.R
ChIPseq_RNA_comparison.R
 
 
ChIPseq_annotate_genes.sh
ChIPseq_annotate_genes.sh
 
 
ChIPseq_compare_conditions.sh
ChIPseq_compare_conditions.sh
 
 
ChIPseq_macs.sh
ChIPseq_macs.sh
 
 
ChIPseq_macs_all.sh
ChIPseq_macs_all.sh
 
 
ChIPseq_motifs.R
ChIPseq_motifs.R
 
 
ChIPseq_motifs.sh
ChIPseq_motifs.sh
 
 
ChIPseq_process_rep.sh
ChIPseq_process_rep.sh
 
 
ChIPseq_process_rep_all.sh
ChIPseq_process_rep_all.sh
 
 
ChIPseq_samples.txt
ChIPseq_samples.txt
 
 
ChIPseq_sat_v_exp_peaks.R
ChIPseq_sat_v_exp_peaks.R
 
 
HAS1pr-TDA1pr.fa
HAS1pr-TDA1pr.fa
 
 
HAS1pr-TDA1pr.genome
HAS1pr-TDA1pr.genome
 
 
Hi-C.R
Hi-C.R
 
 
LICENSE
LICENSE
 
 
MCAST_hits.R
MCAST_hits.R
 
 
README.md
README.md
 
 
Rgt1_10aaD.R
Rgt1_10aaD.R
 
 
Rgt1_10aaD_annotations.txt
Rgt1_10aaD_annotations.txt
 
 
Rgt1_10aaD_associations.txt
Rgt1_10aaD_associations.txt
 
 
Rgt1_10aaD_samples.txt
Rgt1_10aaD_samples.txt
 
 
Rgt1_IUPred2.txt
Rgt1_IUPred2.txt
 
 
Rgt1_domains.txt
Rgt1_domains.txt
 
 
Rgt1_mutations.txt
Rgt1_mutations.txt
 
 
Rgt1_muts.R
Rgt1_muts.R
 
 
Rgt1_muts_annotations.txt
Rgt1_muts_annotations.txt
 
 
Rgt1_muts_associations.txt
Rgt1_muts_associations.txt
 
 
Rgt1_muts_samples.txt
Rgt1_muts_samples.txt
 
 
Rgt1_muts_schematic.R
Rgt1_muts_schematic.R
 
 
ScRNAseq.R
ScRNAseq.R
 
 
ScRNAseq.sh
ScRNAseq.sh
 
 
ScRNAseq_all.sh
ScRNAseq_all.sh
 
 
ScRNAseq_samples.txt
ScRNAseq_samples.txt
 
 
ScRNAseq_table.txt
ScRNAseq_table.txt
 
 
ScSu.32000.bed
ScSu.32000.bed
 
 
ScSu.32000.bin_annotations.txt
ScSu.32000.bin_annotations.txt
 
 
ScSu.32000.chr_annotations.txt
ScSu.32000.chr_annotations.txt
 
 
ScSuRNAseq.R
ScSuRNAseq.R
 
 
ScSuRNAseq.sh
ScSuRNAseq.sh
 
 
ScSuRNAseq_all.sh
ScSuRNAseq_all.sh
 
 
ScSuRNAseq_samples.txt
ScSuRNAseq_samples.txt
 
 
ScSuRNAseq_table.txt
ScSuRNAseq_table.txt
 
 
WT_RNAseq.R
WT_RNAseq.R
 
 
WT_RNAseq_table.txt
WT_RNAseq_table.txt
 
 
alignment.txt
alignment.txt
 
 
alignment_schematic.R
alignment_schematic.R
 
 
annotate_mutations
annotate_mutations
 
 
annotate_mutations.cpp
annotate_mutations.cpp
 
 
barcode_analysis.sh
barcode_analysis.sh
 
 
count_mutations.py
count_mutations.py
 
 
error-prone.R
error-prone.R
 
 
error-prone.fa
error-prone.fa
 
 
error-prone.sh
error-prone.sh
 
 
error-prone_all.sh
error-prone_all.sh
 
 
error-prone_samples.txt
error-prone_samples.txt
 
 
fixed-locus_MAP-C_all.sh
fixed-locus_MAP-C_all.sh
 
 
fixed-locus_ko.R
fixed-locus_ko.R
 
 
fixed-locus_ko_annotations.txt
fixed-locus_ko_annotations.txt
 
 
fixed-locus_ko_associations.txt
fixed-locus_ko_associations.txt
 
 
fixed-locus_ko_barcodes.fa
fixed-locus_ko_barcodes.fa
 
 
fixed-locus_ko_samples.txt
fixed-locus_ko_samples.txt
 
 
gene_lengths.sh
gene_lengths.sh
 
 
get_max.py
get_max.py
 
 
in-gene_ko.R
in-gene_ko.R
 
 
in-gene_ko.sh
in-gene_ko.sh
 
 
in-gene_ko_TF_positions.txt
in-gene_ko_TF_positions.txt
 
 
in-gene_ko_all.sh
in-gene_ko_all.sh
 
 
in-gene_ko_annotations.txt
in-gene_ko_annotations.txt
 
 
in-gene_ko_barcodes.fa
in-gene_ko_barcodes.fa
 
 
in-gene_ko_cendist.txt
in-gene_ko_cendist.txt
 
 
in-gene_ko_groups.txt
in-gene_ko_groups.txt
 
 
in-gene_ko_positions.txt
in-gene_ko_positions.txt
 
 
in-gene_ko_samples.txt
in-gene_ko_samples.txt
 
 
interactor_ko.R
interactor_ko.R
 
 
interactor_ko_annotations.txt
interactor_ko_annotations.txt
 
 
interactor_ko_associations.txt
interactor_ko_associations.txt
 
 
interactor_ko_samples.txt
interactor_ko_samples.txt
 
 
matrices.txt
matrices.txt
 
 
motif_Leu3.txt
motif_Leu3.txt
 
 
motif_Rgt1.txt
motif_Rgt1.txt
 
 
motif_Sdd4.txt
motif_Sdd4.txt
 
 
motif_analysis.sh
motif_analysis.sh
 
 
motif_pad.py
motif_pad.py
 
 
motif_rc.py
motif_rc.py
 
 
motifs_Leu3_Sdd4_Rgt1.txt
motifs_Leu3_Sdd4_Rgt1.txt
 
 
plotting_refs.txt
plotting_refs.txt
 
 
primers.txt
primers.txt
 
 
read_end_position
read_end_position
 
 
read_end_position.cpp
read_end_position.cpp
 
 

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MAP-C

Code and annotation files used to generate figures for Kim et al, "A combination of transcription factors mediates inducible interchromosomal contacts" eLife 2019 https://elifesciences.org/articles/42499.

Data from https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE118118; for Hi-C data (Hi-C.R) and RNA-seq data of wild type S. cerevisiae in saturated and exponential growth conditions (WT_RNAseq.R), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE88952; and for microarray gene expression data of leu3D (ylr451w), sdd4D (ypr022c), and rgt1D (ykl038w), https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE4654.

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Code and annotation files for MAP-C paper

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