PavlidisLab/rdp

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

Language: Java - Size: 21.4 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 5 - Forks: 8

PavlidisLab/ermineJ

Analysis of enrichment of gene sets with a GUI and CLI

Language: Java - Size: 47.7 MB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

PavlidisLab/gsec

Reusable implementation of the Spring Security framework for lab projects

Language: Java - Size: 454 KB - Last synced at: 4 days ago - Pushed at: 4 days ago - Stars: 0 - Forks: 0

PavlidisLab/gemma.R

An R wrapper for the Gemma RESTful API

Language: R - Size: 85.3 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 10 - Forks: 1

PavlidisLab/sc-annotation-pipeline

Language: Python - Size: 116 MB - Last synced at: 5 days ago - Pushed at: 5 days ago - Stars: 0 - Forks: 0

PavlidisLab/Gemma

Genomics data re-analysis

Language: Java - Size: 485 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 23 - Forks: 6

PavlidisLab/baseCode

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

Language: Java - Size: 33.3 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 4 - Forks: 0

PavlidisLab/GemBrow

The Gemma Browser

Language: Vue - Size: 2.9 MB - Last synced at: 3 days ago - Pushed at: 3 days ago - Stars: 4 - Forks: 1

PavlidisLab/pavlab-starter-parent

Curated dependencies for the Pavlidis Lab's Java applications

Size: 160 KB - Last synced at: 17 days ago - Pushed at: 17 days ago - Stars: 0 - Forks: 0

PavlidisLab/rnaseq-pipeline

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

Language: Shell - Size: 43.6 MB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 24 - Forks: 5

PavlidisLab/bioluigi

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Language: Python - Size: 121 KB - Last synced at: 23 days ago - Pushed at: 23 days ago - Stars: 9 - Forks: 0

PavlidisLab/coex-simulation

A theoretical study on the detection of dynamic gene regulation in bulk tissue transcriptomes.

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PavlidisLab/TGEMO

The Gemma Ontology

Language: Python - Size: 99.6 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 1 - Forks: 1

PavlidisLab/gemmapy

Language: Python - Size: 5.39 MB - Last synced at: about 1 month ago - Pushed at: 3 months ago - Stars: 6 - Forks: 1

PavlidisLab/aggtools

Language: R - Size: 98.6 KB - Last synced at: 18 days ago - Pushed at: 4 months ago - Stars: 0 - Forks: 0

PavlidisLab/TR_singlecell

This repo contains the code for my paper on reproducible TR coexpression patterns using single cell RNA-seq

Language: R - Size: 1.04 MB - Last synced at: 18 days ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

PavlidisLab/GemmaAnalysis

Code used for some analyses of data in Gemma. Probably not of general utility!

Language: Java - Size: 1000 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

PavlidisLab/GemmaDE

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

Language: R - Size: 76.1 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 4 - Forks: 0

PavlidisLab/ermineR

R wrapper for ermineJ

Language: R - Size: 60.3 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 6 - Forks: 4

PavlidisLab/TR_aggregation

Contains the code for "Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets"

Language: R - Size: 20.3 MB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 1

PavlidisLab/aggregate_microglia

This project looks to aggregate single cell coexpression patterns for microglial datasets

Language: R - Size: 310 KB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

PavlidisLab/Unibind_analysis

Leveraging data from the Unibind database.

Language: R - Size: 88.9 KB - Last synced at: 18 days ago - Pushed at: 6 months ago - Stars: 0 - Forks: 0

PavlidisLab/neuroexpresso

:bar_chart: Gene expression in neuroexpresso database

Language: R - Size: 339 MB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 18 - Forks: 1

PavlidisLab/SFARI_project

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PavlidisLab/ndb

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

Language: Java - Size: 990 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 0

PavlidisLab/McDiarmid-etal-2019_Multi-Worm-Tracker-analysis

Analysis code for "Systematic phenomics analysis of ASD-associated genes reveals shared functions and parallel networks underlying reversible impairments in habituation learning" (DOI: 10.1101/687194)

Language: R - Size: 152 KB - Last synced at: over 1 year ago - Pushed at: almost 6 years ago - Stars: 0 - Forks: 0

PavlidisLab/patchSeqQCManuscript

Quality Control measures for patch-seq data using marker genes

Language: R - Size: 87.7 MB - Last synced at: over 1 year ago - Pushed at: about 7 years ago - Stars: 0 - Forks: 1

PavlidisLab/searchGEO

Language: MATLAB - Size: 152 KB - Last synced at: over 1 year ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

PavlidisLab/pnas-parkinsons

Supplementary information on the re-analysis of Santiago and Potashkin 2015.

Size: 52.8 MB - Last synced at: over 1 year ago - Pushed at: over 10 years ago - Stars: 0 - Forks: 0

PavlidisLab/jenkins-replication-checksum Fork of JacobsonMT/jenkins-replication-checksum

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

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PavlidisLab/matrix2png

Language: C - Size: 557 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

PavlidisLab/SFARI-ASD_Gene_Selection

ASD gene selection/prioritization pipeline for SFARI project. Ref Aim 1.1

Language: Python - Size: 123 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 0 - Forks: 0

PavlidisLab/Post-PTEN

Data analysis for Post et al. 2019, "Multi-model functionalization of disease-associated PTEN missense mutations identifies multiple molecular mechanisms underlying protein dysfunction."

Language: R - Size: 30.3 KB - Last synced at: over 1 year ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

PavlidisLab/VariCarta

Repository for VariCarta data releases

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PavlidisLab/GeoBrainFinder

Language: MATLAB - Size: 81.1 KB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

PavlidisLab/CellularComposition

Material for paper "Untangling the effects of cellular composition on coexpression analysis", Farahbod&Pavlidis 2020

Language: MATLAB - Size: 16.1 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 1 - Forks: 0

PavlidisLab/Gemma-rest-web

Gemma REST API interactive documentation website

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PavlidisLab/GEOMMTx

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PavlidisLab/directed-studies-fiel

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PavlidisLab/gemmaBackups

Functions to store and access backups of Gemma API outputs

Language: R - Size: 78.1 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

PavlidisLab/CMap-Evaluation

Evaluation of CMap 1 (Lamb et al. 2006) and CMap 2/LINCS-L1000 (Subramanian et al. 2017)

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PavlidisLab/Bioinf_2019

Farahbod & Pavlidis 2019 Bioinformatics

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PavlidisLab/ASDMachineLearning

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PavlidisLab/gemmaDifExpDump

Downloads all all differential expression in Gemma for analysis

Language: R - Size: 16.6 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

PavlidisLab/patchSeqQC

Quality control for patch-seq data using marker genes

Language: R - Size: 3.44 MB - Last synced at: over 1 year ago - Pushed at: almost 7 years ago - Stars: 2 - Forks: 1

PavlidisLab/slack-zotero Fork of JacobsonMT/slack-zotero

Simple interface between Slack Webhooks and Zotero API

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PavlidisLab/jenkins-db-backup Fork of JacobsonMT/jenkins-db-backup

Generic script used to backup and maintain recent archives of a database through Jenkins

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PavlidisLab/regenerationCMap

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PavlidisLab/pavlab-parent

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PavlidisLab/markerGeneProfile

Marker gene profile estimation method used in NeuroExpresso manuscript

Language: R - Size: 33.7 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 12 - Forks: 2

PavlidisLab/gene2pubmed-stats

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PavlidisLab/neuroExpressoAnalysis

Paper at: http://www.eneuro.org/content/4/6/ENEURO.0212-17.2017

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PavlidisLab/transcriptomic_correlates

Materials related to "Transcriptomic correlates of electrophysiological and morphological diversity within and across neuron types"

Language: Jupyter Notebook - Size: 88.2 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 6 - Forks: 2

PavlidisLab/luigi Fork of spotify/luigi

Luigi is a Python module that helps you build complex pipelines of batch jobs. It handles dependency resolution, workflow management, visualization etc. It also comes with Hadoop support built in.

Language: Python - Size: 10.1 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

PavlidisLab/rnaseq-variant-pipeline

Pipeline for calling and analyzing variants from RNA-Seq data

Language: Python - Size: 15.6 KB - Last synced at: over 1 year ago - Pushed at: almost 3 years ago - Stars: 1 - Forks: 0

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.

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PavlidisLab/gotrack

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

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PavlidisLab/dtri-curation

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PavlidisLab/GemmaPaper-2020

Paper on the Gemma Framework (https://gemma.msl.ubc.ca/home.html)

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PavlidisLab/ANEVA-DOT Fork of PejLab/ANEVA-DOT

Tests Allelic Expression data for extreme imbalance w.r.t. population

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PavlidisLab/bioconda-recipes Fork of bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

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PavlidisLab/AlzMouseModelMeta

AD_mouse_model_project

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PavlidisLab/neuroExpressoData

A package that only includes mouse cell type expression datasets used for Mancarci et al. 2017 paper. Data is directly acquired from neuroExpressoAnalysis repository

Language: R - Size: 105 MB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

PavlidisLab/RSEM Fork of deweylab/RSEM

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

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PavlidisLab/gemmaMGP

shiny app to calculate marker gene profiles for gemma studies (WIP)

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