Data

Expression data

Expression values (gene counts and CPM) for all quads at all timepoints are in:

• counts_strand_comb.Rdata
• cpm_strand_comb.Rdata

Allele specific expression data can be found in:

• exprs_all.Rdata

Phenotypes and metadata

• armadillo_hem.Rdata
• metadata.Rdata

Genotype information

• snps_overlaps.Rdata

Analysis outputs

Testing/training splits for identity analysis

• ase_ratios.test_train.Rdata
• cpm_test_train.Rdata

Identity analysis

• ase_identity_xscaff.Rdata
• ase_identity_noX.Rdata

Feature genes

• ase.feature.genes.Rdata

XCI skewing estimates

• skew.est.max.genes.Rdata
• estimated_ratios.Rdata

Models for identity analysis

• ase_rand.null.ratios2.xsub.Rdata
• ase_rand.ratios.noX.Rdata
• final.model.Rdata

SNP binomial modeling analyses

• black_list_homo_snps.rds
• ase_cov.rds The remaining files are too large to be uploaded here, but can be located at:

Other data

Genome annotation

• gene_annotations_v0_95_mod.Rdata Functional gene sets:
• GO.arm.Rdata Homologs:
• homologs.Rdata X chromosome chains and objects
• chrX.chainHg38.txt.gz
• chrX.chainMm10.txt.gz
• chromInfo.txt.gz
• cytoBandIdeo.txt.gz

Code

See notebooks and the bin for all the analyses and scripts.