Discover PavlidisLab/transcriptomic_correlates Open Source project

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PavlidisLab

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

rnaseq-pipeline

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

Python

Gemma

Genomics data re-analysis

Java

neuroexpresso

📊 Gene expression in neuroexpresso database

markerGeneProfile

Marker gene profile estimation method used in NeuroExpresso manuscript

gemma.R

An R wrapper for the Gemma RESTful API

neuroExpressoAnalysis

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

bioluigi

Reusable and maintained Luigi tasks to incorporate in bioinformatics pipelines

Python

gemmapy

Python

ermineR

R wrapper for ermineJ

baseCode

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

Java

rdp

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

Java

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.

Java

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.

JavaScript

GemBrow

The Gemma Browser

Vue

VariCarta

Repository for VariCarta data releases

CMap-Evaluation

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

patchSeqQC

Quality control for patch-seq data using marker genes

gotrack

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

Java

Gemma-rest-web

Gemma REST API interactive documentation website

HTML

CellularComposition

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

TGEMO

SFARI_project

AlzMouseModelMeta

AD_mouse_model_project

rnaseq-variant-pipeline

Pipeline for calling and analyzing variants from RNA-Seq data

Python

matrix2png

PavlidisLab/transcriptomic_correlates

PavlidisLab

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