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/rnaseq-pipeline
RNA-seq pipeline for raw sequence alignment and transcript/gene quantification.
PavlidisLab/Gemma
Genomics data re-analysis
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/GemBrow
The Gemma Browser
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/sc-annotation-pipeline
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
This repo contains the code for my paper on reproducible TR coexpression patterns using single cell RNA-seq
PavlidisLab/Unibind_analysis
Leveraging data from the Unibind database.
PavlidisLab/aggregate_microglia
This project looks to aggregate single cell coexpression patterns for microglial datasets
PavlidisLab/aggtools
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/owlviz
A Protégé Desktop plugin that provides a graphical representation of the class hierarchy in an OWL ontology.
PavlidisLab/pavlab-starter-parent
Curated dependencies for the Pavlidis Lab's Java applications