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Source code for "A comparative study of endoderm differentiation in humans and chimpanzees"

Lauren Blake; Samantha M. Thomas; John D. Blischak; Chiawen Joyce Hsaio; Claudia Chavarria; Marsha Myrthil; Yoav Gilad; Bryan Pavlovic

Source code for the publication, "A comparative study of endoderm differentiation in humans and chimpanzees". 

LEB was supported by the National Science Foundation Graduate Research Fellowship (DGE-1144082) and by the Genetics and Gene Regulation Training Grant (T32 GM07197). BJP was supported by the Training in Emerging Multidisciplinary Approaches to Mental Health and Disease (T32MH020065). This work was funded by an NIH grant from NIGMS (MH084703). The content presented in this article is solely the responsibility of the authors and the funding bodies had no role in the design of the study and collection, analysis, interpretation of data, and in writing the manuscript.
Files (62.7 MB)
Name Size
After_removal_sample_info.csv
md5:51bd9fb52986c321b3af8b345a1a9d44
2.0 kB Download
Analysis_purity_information.Rmd
md5:e2c73d9a286e1b6d88f923fff74a7ca7
37.4 kB Download
Compare_methods_combining_technical_replicates_cyclic_loess.Rmd
md5:8b7d444c9dfd9a380ef9f11a4e4ced11
24.2 kB Download
Cormotif_avg_log2_CPM_cyclic_loess_new.Rmd
md5:b8670e03debd8391a4df32788ab1feb9
27.8 kB Download
cpm_cyclicloess.txt
md5:1b3d26bb011d695f10b98b8aa7667f09
11.2 MB Download
cpm_cyclicloess_40.txt
md5:ee450b8754bddda84192ea58006072d6
7.2 MB Download
DE_exp_limma_only_cyclic_loess.Rmd
md5:f1ae495696ebf2652baf6df34a86267c
100.9 kB Download
Endo_TC_Data_Share_Sorting.csv
md5:6df48dc53b6ea6cd62d8df9df925a0ae
23.0 kB Download
Endoderm_mapping_2_core_runs.csv
md5:6b143ab16f8dafbbd68876b8caae8607
7.0 kB Download
Endoderm_mapping_core_1.csv
md5:de25554fa297491596a4ed58cdfe6841
4.8 kB Download
Endoderm_mapping_core_2.csv
md5:8067a253bf77ad2cb2682093c4e32fc0
4.5 kB Download
Endoderm_TC_core_runs.Rmd
md5:d635ee1ce4b0a2243cda5c7b6ae2f9d5
36.4 kB Download
exon.ortho.hg19.gff
md5:64ebc9e0a61dc002f3f46418c279acd1
13.0 MB Download
exon.ortho.panTro3.gff
md5:e15edb021b2e5f79d43a431b0353e84d
13.0 MB Download
fqTrim1.py
md5:fec66bc011878e438d536a37dc53517a
1.8 kB Download
gene_counts_combined.txt
md5:60a2a640636fa99f623f5c9ec6e0c430
6.1 MB Download
gene_counts_cutoff_norm_data.txt
md5:76d5d06f56518ae074c22bf00615b85b
3.0 MB Download
Gene_ID_Conversion.csv
md5:1fcbc17bcff35bf0b8a2188193a76248
241.8 kB Download
GO_enrichment_cyclic_loess.Rmd
md5:2bce3e84ff4fb6b3060c7cb64fb08095
2.8 kB Download
GO_motif_analysis.Rmd
md5:2832ef03f3aef2bbcbd8c7c5732f2296
9.0 kB Download
Lethality_analysis.Rmd
md5:af338f40826102cd6d293d28594f5737
4.4 kB Download
Make_figures.R
md5:46b37e41b0bdfc626422cfb0c80f0a49
20.9 kB Download
mapping_to_orthologous_exons_pipeline.sh
md5:3c8fe785865222078b7826b1c7bad2eb
2.1 kB Download
ortho_exon_lengths.txt
md5:1302c8cacd5d3d0e541d13204b37d6fa
404.4 kB Download
Red_var_genes.Rmd
md5:6a11768d2774905c21f612b215359bad
32.7 kB Download
RPKM_analysis.Rmd
md5:f62bf29330be69e3a5b8ffca2329c240
22.4 kB Download
samplefactors-filtered.txt
md5:785b36b6fe4f2ac5c69124df76bad366
1.2 kB Download
STEM_post_filtering_ensg_only.txt
md5:086a30dd05063baee669298fd48c668a
63.0 kB Download
Technical_factor_analysis_cyclic_loess.Rmd
md5:e873aeb37b5c3d55eac597637b441cb9
30.6 kB Download
Technical_factors_across_days.Rmd
md5:2b287fcfa4e561a7204e60bdd533c508
13.3 kB Download
Temporal_changes_variation_cyclicloess.Rmd
md5:f40dcd8d536c89ad38591360a29097e5
254.1 kB Download
TMM- and cyclic loess-normalized log2 counts per million (CPM) values .csv
md5:c549cbe453a165f7144a942a3e72a059
8.0 MB Download
Variance_compared_to_GTEx.Rmd
md5:bc61f48989901db9af412d5299b0cb80
5.8 kB Download
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