Pavlidis lab

rnaseq-pipeline

RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.

Gemma

Genomics data re-analysis

neuroexpresso

:bar_chart: Gene expression in neuroexpresso database

bioluigi

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

gemma.R

An R wrapper for the Gemma RESTful API

baseCode

Data structures, math and statistics tools, and utilities that are often needed across projects.

gemmapy

rdp

Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network

aspiredb

ASPIREdb is a web-based software system for the analysis of genomic variants (CNVs, SNVs, and Indels) and phenotypes. Potential users include researchers who are trying to understand the relationships between discovered variants and phenotypes.

GemmaDE

Discover biological conditions associated with differential gene expression by compiling information from >10,000 published experiments

ndb

Web application and database providing a harmonized and comprehensive collection of genetic variants published in peer-reviewed literature.

GemBrow

The Gemma Browser

gotrack

Web-based system and database that provides access to historical records and trends in the Gene Ontology and GO annotations

RSEM

RSEM with STAR shared memory support (fork from RSEM: accurate quantification of gene and isoform expression from RNA-Seq data)

SFARI_project

TGEMO

The Gemma Ontology

ermineJ

Analysis of enrichment of gene sets with a GUI and CLI

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

gsec

Reusable implementation of the Spring Security framework for lab projects

jenkins-replication-checksum

Perform replication integrity checksum using Percona pt-table-checksum in a CI environment.

matrix2png

pavlab-parent

pavlab-starter-parent

Curated dependencies for the Pavlidis Lab's Java applications

regenerationCMap

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"

TR_singlecell

Unibind_analysis

Leveraging data from the Unibind database.