Pavlidis lab
The Pavlidis Lab at the University of British Columbia
Vancouver, British Columbia, Canada
Pinned Repositories
bioluigi
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
ermineR
R wrapper for ermineJ
Gemma
Genomics data re-analysis
gemma.R
An R wrapper for the Gemma RESTful API
gemmapy
markerGeneProfile
Marker gene profile estimation method used in NeuroExpresso manuscript
neuroexpresso
:bar_chart: Gene expression in neuroexpresso database
neuroExpressoAnalysis
Paper at: http://www.eneuro.org/content/4/6/ENEURO.0212-17.2017
rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
transcriptomic_correlates
Materials related to "Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron types"
Pavlidis lab's Repositories
PavlidisLab/Gemma
Genomics data re-analysis
PavlidisLab/rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
PavlidisLab/neuroexpresso
:bar_chart: Gene expression in neuroexpresso database
PavlidisLab/gemma.R
An R wrapper for the Gemma RESTful API
PavlidisLab/bioluigi
Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines
PavlidisLab/ermineR
R wrapper for ermineJ
PavlidisLab/gemmapy
PavlidisLab/baseCode
Data structures, math and statistics tools, and utilities that are often needed across projects.
PavlidisLab/rdp
Researcher Gene Registry. Originally developed for the Canadian Rare Disease Models & Mechanisms Network
PavlidisLab/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.
PavlidisLab/GemBrow
The Gemma Browser
PavlidisLab/GemmaDE
Discover biological conditions associated with differential gene expression by compiling information from >10,000 published experiments
PavlidisLab/ndb
Web application and database providing a harmonized and comprehensive collection of genetic variants published in peer-reviewed literature.
PavlidisLab/gotrack
Web-based system and database that provides access to historical records and trends in the Gene Ontology and GO annotations
PavlidisLab/RSEM
RSEM with STAR shared memory support (fork from RSEM: accurate quantification of gene and isoform expression from RNA-Seq data)
PavlidisLab/SFARI_project
PavlidisLab/TGEMO
The Gemma Ontology
PavlidisLab/coex-simulation
A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.
PavlidisLab/ermineJ
Analysis of enrichment of gene sets with a GUI and CLI
PavlidisLab/GemmaAnalysis
Code used for some analyses of data in Gemma. Probably not of general utility!
PavlidisLab/gemmaBackups
Functions to store and access backups of Gemma API outputs
PavlidisLab/gemmaDifExpDump
Downloads all all differential expression in Gemma for analysis
PavlidisLab/gsec
Reusable implementation of the Spring Security framework for lab projects
PavlidisLab/jenkins-replication-checksum
Perform replication integrity checksum using Percona pt-table-checksum in a CI environment.
PavlidisLab/pavlab-parent
PavlidisLab/pavlab-starter-parent
Curated dependencies for the Pavlidis Lab's Java applications
PavlidisLab/regenerationCMap
PavlidisLab/TR_aggregation
Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"
PavlidisLab/TR_singlecell
PavlidisLab/Unibind_analysis
Leveraging data from the Unibind database.