Data from: Immune genes are hotspots of shared positive selection across birds and mammals

Shultz AJ, Sackton T

Date Published: January 9, 2019

DOI: https://doi.org/10.5061/dryad.kt24554

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Alignments used for comparative genomics
Downloaded 15 times
Description Multiple species alignment for each HOG. NCBI gene IDs for HOGs can be found in R_data_and_scripts/02_output_annotated_data/raw_results_sptrees_all_annotations.csv from zipped R_data_and_scripts file.
Download comparative_genomics_hog_alignments.zip (94.41 Mb)
Details View File Details
Title R Scripts and Data Files
Downloaded 25 times
Description All selection scan and differential expression results (PAML results, HyPhy results, Sleuth results), and all scripts for subsequent analyses. There are seven modules that include and R script, directory with any necessary input data, and directory with any output files. The scripts do the following: 1. process all PAML and HyPhy output into analysis-ready formats. 2. Annotate all HOGs with NCBI and Ensembl gene IDs. 3. General dataset statistic calculations 4. Bird KEGG pathway enrichment analyses. 5. Comparisons of bird and mammal selection scan results 6. Clustering and analysis of bird aBS-REL results. 7. Transcriptome analyses for both birds and mammals.
Download R_data_and_scripts.zip (368.9 Mb)
Details View File Details

When using this data, please cite the original publication:

Shultz AJ, Sackton T (2019) Immune genes are hotspots of shared positive selection across birds and mammals. eLife 8: e41815. https://doi.org/10.7554/eLife.41815

Additionally, please cite the Dryad data package:

Shultz AJ, Sackton T (2019) Data from: Immune genes are hotspots of shared positive selection across birds and mammals. Dryad Digital Repository. https://doi.org/10.5061/dryad.kt24554
Cite | Share
Download the data package citation in the following formats:
   RIS (compatible with EndNote, Reference Manager, ProCite, RefWorks)
   BibTex (compatible with BibDesk, LaTeX)

Search for data

Be part of Dryad

We encourage organizations to: