timoast/Arabidopsis-TE-variants-1.zip
timoast-Arabidopsis-TE-variants-477b7ea
.gitignore
848 Bytes
AnalysisCode
README.md
3.3 kB
RNA_heatmaps.R
4.2 kB
TE_DMR_analysis.R
21.3 kB
TE_genomic_features.Rmd
6.6 kB
TE_insertion_distribution.R
15.1 kB
basho.Rmd
2.5 kB
burden_mC_DMRs.R
7.2 kB
coverage_vs_variants.R
1.9 kB
family_enrichment.R
10.2 kB
flanking_mC_correlations.R
4.2 kB
gene_expression_burden.R
9.0 kB
gene_expression_volcano.R
8.7 kB
kee_regions.R
693 Bytes
mC_heatmap.R
10.2 kB
plot_trans_scatter.R
3.5 kB
quadrana_overlap.sh
252 Bytes
resistance_phenotype.R
1.7 kB
run_trans_analysis.sh
1.5 kB
trans_dmr_pval.R
6.0 kB
variants_per_accession.R
2.5 kB
DataAquisition
README.md
61 Bytes
TEPID_master_script.sh
1.8 kB
build_tables.py
4.7 kB
false_negative_estimation.md
3.1 kB
get_DHS_data.sh
159 Bytes
source_PE_data.sh
667 Bytes
source_RNA_data.sh
84 Bytes
source_mC_data.sh
476 Bytes
LICENSE
35.1 kB
ProcessedData
DNAmethylation
bud_vs_leaf_allC_deletions.tsv.gz
800.3 kB
bud_vs_leaf_allC_insertions.tsv.gz
1.2 MB
flanking_CG.tsv.gz
3.3 MB
flanking_CG_no_insertion.tsv.gz
1.9 MB
flanking_CG_true_deletions.tsv.gz
909.4 kB
flanking_CHG.tsv.gz
3.3 MB
flanking_CHG_no_insertion.tsv.gz
1.9 MB
flanking_CHG_true_deletions.tsv.gz
934.2 kB
flanking_CHH.tsv.gz
4.0 MB
flanking_CHH_no_insertion.tsv.gz
2.3 MB
flanking_CHH_true_deletions.tsv.gz
1.1 MB
flanking_allC.tsv.gz
4.1 MB
flanking_allC_no_insertion.tsv.gz
2.4 MB
flanking_allC_true_deletions.tsv.gz
1.1 MB
flanking_allc_200_bp.tsv.gz
4.2 MB
flanking_mc_correlations.txt
244.1 kB
GeneFeatures
dhs_intersections.bed.gz
127.7 kB
exon_intersections.bed.gz
614.9 kB
exons.bed.gz
1.4 MB
gene_downstream_regions.bed.gz
517.0 kB
gene_downstream_regions_intersections.bed.gz
670.6 kB
gene_upstream_regions.bed.gz
516.7 kB
gene_upstream_regions_intersections.bed.gz
796.2 kB
genomic_features.bed.gz
400.4 kB
intergenic_intersections.bed.gz
2.0 MB
intergenic_regions.bed.gz
556.9 kB
intron_intersections.bed.gz
159.6 kB
introns.bed.gz
739.3 kB
pseudogene.bed.gz
17.8 kB
pseudogene_intersections.bed.gz
26.0 kB
te_intersections.bed.gz
1.2 MB
utr3.bed.gz
259.9 kB
utr3_intersections.bed.gz
55.1 kB
utr5.bed.gz
281.8 kB
utr5_intersections.bed.gz
31.9 kB
KEE_intersection_count.tsv
303 Bytes
README.md
45 Bytes
TEPAV_no_insertion.tsv.gz
733.3 kB
TEPAV_true_deletions.tsv.gz
339.1 kB
TE_CG_DMR_distances.bed.gz
1.5 MB
TE_C_DMR_distances.bed.gz
848.3 kB
TE_deletions_matrix.tsv.gz
201.3 kB
TE_insertions_matrix.tsv.gz
390.8 kB
c_dmr_allC.tsv.gz
3.9 MB
c_dmr_correlations.tsv.gz
1.0 MB
c_dmr_intersections.tsv.gz
112.4 kB
c_dmr_mc_ranks.tsv.gz
3.4 MB
c_dmr_tepav_distance.tsv.gz
129.7 kB
c_dmrs_closest_te.tsv.gz
156.4 kB
cdmr_sig_pvals.tsv
5.8 MB
cg_dmr_correlations.tsv.gz
1.8 MB
cg_dmr_intersections.tsv.gz
321.2 kB
cg_dmr_mc_ranks.tsv.gz
8.4 MB
cg_dmrs_allC.tsv.gz
11.4 MB
coverages.tsv
1.9 kB
deletion_counts.tsv
2.4 kB
deletion_stats.tsv
165 Bytes
dmr_overlaps.tsv
220 Bytes
expression_ranks.tsv.gz
5.0 MB
family_enrichments.tsv
15.2 kB
gene_feature_counts.csv
999 Bytes
gene_list.tsv
1.0 MB
ghost_trans_associations.tsv
4.5 kB
insertion_counts.tsv
2.2 kB
kee_pvals.tsv
408 Bytes
kee_random_10k.bed
220.7 kB
kee_random_intersections.bed
252.5 kB
poly_te_genotyped.tsv.gz
1.4 MB
random_coords.bed
508.7 kB
random_coords_closest_c_dmr.bed.gz
205.0 kB
random_coords_closest_c_dmr_deletions.bed.gz
191.3 kB
random_coords_closest_c_dmr_insertions.bed.gz
200.9 kB
random_coords_closest_c_dmr_intermediate.bed.gz
181.5 kB
random_coords_closest_cg_dmr.bed.gz
572.5 kB
random_coords_closest_cg_dmr_deletions.bed.gz
528.2 kB
random_coords_closest_cg_dmr_insertions.bed.gz
558.1 kB
random_coords_closest_cg_dmr_intermediate.bed.gz
511.3 kB
random_coords_deletions.bed
129.0 kB
random_coords_insertions.bed
332.2 kB
random_coords_intermediate.bed
47.6 kB
random_selections_c_dmr_rep_10k.txt
90.0 kB
random_selections_c_dmr_rep_10k_deletions.txt
90.0 kB
random_selections_c_dmr_rep_10k_insertions.txt
90.0 kB
random_selections_c_dmr_rep_10k_intermediate.txt
90.0 kB
random_selections_cg_dmr_rep_10k.txt
90.0 kB
random_selections_cg_dmr_rep_10k_deletions.txt
90.0 kB
random_selections_cg_dmr_rep_10k_insertions.txt
90.0 kB
random_selections_cg_dmr_rep_10k_intermediate.txt
90.0 kB
refinement_stats.tsv
1.9 kB
sig_genes.tsv
28.7 kB
superfamily_enrichments.tsv
881 Bytes
ProcessingCode
README.md
2.4 kB
add_dmr_features.sh
1.7 kB
add_feature_between.py
1.7 kB
bootstrap_te_variants.sh
5.2 kB
choose_random_coords.py
409 Bytes
classify_TE_absence.R
2.2 kB
closest_DMRs.sh
393 Bytes
filter_sig_pvals_correlated_tes.sh
1.7 kB
flanking_mc_correlations.R
6.3 kB
gene_flanking.py
1.5 kB
get_counts.py
242 Bytes
get_cov.py
391 Bytes
get_coverages_all_accessions.sh
540 Bytes
get_mc_200bp_all_accessions.py
3.0 kB
get_mc_DMRs.py
3.0 kB
get_mc_DMRs_context.py
3.3 kB
get_mc_bud_vs_leaf.py
6.4 kB
get_mc_dmrs.sh
1.5 kB
get_mc_flanking.py
6.0 kB
get_mc_te.py
5.9 kB
intersect_KEE_regions.sh
456 Bytes
long_range_ld.py
3.1 kB
make_gene_list.sh
186 Bytes
make_genomic_feature_files.sh
7.1 kB
no_te_genes.gff
43.6 MB
reformat_tepav_matrix.py
2.3 kB
run_flanking_mc.sh
2.9 kB
simulated_TE_variants
RSVSim_commands.R
2.6 kB
generate_sim_coords.py
4.3 kB
sim_reads.txt
103 Bytes
var_coverage.py
1.4 kB
split_true_deletions.sh
684 Bytes
README.md
392 Bytes
RawData
Gaut_basho_supplement.csv
33.5 kB
KEE_regions_150kb.bed
271 Bytes
Quadrana_TEPAV.tsv.gz
21.5 kB
SraAccList.txt
2.2 kB
Sullivan_DHS_PE_peaks_control.bed.gz
426.3 kB
TAIR10_GFF3_genes.gff.gz
5.0 MB
TAIR9_TE.bed.gz
392.3 kB
TEPID_TEPAV.tsv.gz
1.5 MB
accession_names.tsv
1.3 kB
all_mc_tables.txt
2.5 kB
c_dmrs.tsv.gz
102.9 kB
centromere_positions.txt
110 Bytes
cg_dmrs.tsv.gz
304.9 kB
gene_expression.tsv.gz
13.9 MB
snp_association.tsv.gz
228.2 kB
tair10.fa.gz
36.5 MB