Pavlidis lab's repositories
rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
neuroexpresso
:bar_chart: Gene expression in neuroexpresso database
GemmaAnalysis
Code used for some analyses of data in Gemma. Probably not of general utility!
gemmaBackups
Functions to store and access backups of Gemma API outputs
gemmaDifExpDump
Downloads all all differential expression in Gemma for analysis
jenkins-replication-checksum
Perform replication integrity checksum using Percona pt-table-checksum in a CI environment.
pavlab-starter-parent
Curated dependencies for the Pavlidis Lab's Java applications
SFARI-ASD_Gene_Selection
ASD gene selection/prioritization pipeline for SFARI project. Ref Aim 1.1
TR_aggregation
Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"
Unibind_analysis
Leveraging data from the Unibind database.