Hood-Price Lab for Systems Biomedicine 's repositories
ShannonMets
** Blood metabolome predicts gut microbiome α-diversity in humans**
probannopy
A python package for Probanno!
BrowserViz
base class for igvR and other R/browser packages
chip-seq-motif-study
to determine the how TF motifs do and do not match ChIP-seq assays
ChIPseqMotifMatch
Assess motif match in ChIP-seq bam file
clustergrammerShiny
an R shiny wrapper around the Ma'ayan Lab's clustergrammer javascript heatmap
genomescale_scripts
scripts I use for making genome-scale transcriptional regulatory networks
kg-geneOntology
GO for graph databases
neo4jService
a microservice for queries to biomedical knowledge graphs in Neo4J
regulatoryHAR
explore gene regulatory implications of human accelerated regions of the genome
rnaSeqNormalizer
cory funk's methods for normalizing RNA-seq counts, in preparation for building trena models
spokeExperiments
evaluate the SPOKE graph database
tissueBias
Gina Huynh: A Characterization of Tissue-Specific Gene Bias in Gene Set Collections Used for Pathway Enrichment Analysis
TrenaProject
abstract base class for all TrenaProjects
TrenaProjectADPRN
AD regulatory networks using protein data
TrenaProjectBrainCell
cory's deconvolved rna model building
TrenaProjectHG38.generic
a utility package providing easy access to the shared HG38 data and capabilities, no tissue specificity required
TrenaProjectLiver
support for building regulatory networks based upon gtex liver data
TrenaProjectScerevisiae
model gene regulatory networks in yeast
trenaSGM
A package for building trena single gene models
TrenaValidator
can trena reproduce known (or "known") TF/targetGene relations?
TrenaViz
webapp for creating and exploring trena models