inst/script/instDataReadme.md

In netZoo/netZooR: Unified methods for the inference and analysis of gene regulatory networks

• chip.txt: Yeast Chip-chip data from Glass et al. (https://pubmed.ncbi.nlm.nih.gov/23741402/)

• chip_matched.txt: filtered chip.txt data to include only genes in expr10_matched gene expression file

• expr10_matched.txt: Yeast gene expression data from Glass et al. (https://pubmed.ncbi.nlm.nih.gov/23741402/)

• expr4_matched.txt: Yeast gene expression data from Glass et al. (https://pubmed.ncbi.nlm.nih.gov/23741402/)

• h.all.v6.1.symbols.gmt: Gene Enrichment pathway annotation from GSEA (http://www.gsea-msigdb.org/gsea/msigdb/collections.jsp)

• lioness.py: LIONESS Reticulate Python code from https://github.com/netZoo/netZooPy

• panda.py: PANDA Reticulate Python code from https://github.com/netZoo/netZooPy

• ppi_matched.txt: Protein-Protein Interaction data from STRINGdb v9 (https://string-db.org/)

• Example_2comm.txt: Example of 2 randomly generated networks

• toy_genotype.vcf: Example Variant Call Format file

• toy_map.txt: mapping of gene names from ENSEMBL to symbols

• toy_motif_prior.txt: TF-Gene binding motif generated from Sonawane, Abhijeet Rajendra, et al. "Understanding tissue-specific gene regulation." Cell reports 21.4 (2017): 1077-1088.

• toy_qbic.txt: Variant effect calling sing Qbic Martin, Vincentius, et al. "QBiC-Pred: quantitative predictions of transcription factor binding changes due to sequence variants." Nucleic acids research 47.W1 (2019): W127-W135.

• toy_ppi_prior: Protein-Protein interaction network from STRINGdb (https://string-db.org/)

• toy_eQTL: Expression Quantitaive Trait Locus data file

• toy_expr: gene expression example file

netZoo/netZooR documentation built on June 8, 2024, 6:20 a.m.