RajLabMSSM/mmQTL-pipeline

Language: Python - Size: 1.36 MB - Last synced at: 7 days ago - Pushed at: 7 days ago - Stars: 4 - Forks: 0

RajLabMSSM/leafcutter-pipeline

Differential splicing and visualisation pipeline for the Raj lab

Language: Python - Size: 2.85 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 2 - Forks: 5

RajLabMSSM/downstream-QTL

set of scripts and pipelines to work with QTL results

Language: HTML - Size: 8.07 MB - Last synced at: about 1 month ago - Pushed at: about 1 month ago - Stars: 6 - Forks: 1

RajLabMSSM/isoseq-pipeline

pipeline for working with PacBio long read RNA data using the outputs of isoseq3

Language: Python - Size: 2.2 MB - Last synced at: 19 days ago - Pushed at: 19 days ago - Stars: 5 - Forks: 4

RajLabMSSM/SingleBrain

Size: 882 KB - Last synced at: 2 months ago - Pushed at: 2 months ago - Stars: 0 - Forks: 0

RajLabMSSM/QTL-mapping-pipeline

A snakemake pipeline for QTL mapping. Based on the GTEX pipeline

Language: Python - Size: 2.47 MB - Last synced at: 3 months ago - Pushed at: 3 months ago - Stars: 5 - Forks: 0

RajLabMSSM/echogithub

echoverse module: Extract data and metadata from GitHub

Language: R - Size: 281 KB - Last synced at: 4 months ago - Pushed at: 4 months ago - Stars: 0 - Forks: 1

RajLabMSSM/RajLab_website

Official website for the Raj Lab detailing personnel, updates, current projects and opportunities.

Language: CSS - Size: 388 MB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

RajLabMSSM/MBV_Pipeline

Language: Python - Size: 10.7 KB - Last synced at: 5 months ago - Pushed at: 5 months ago - Stars: 0 - Forks: 0

RajLabMSSM/RNA-pipelines

A repo to contain various RNA-seq processing pipelines, to cut down how many different repos I have.

Language: Python - Size: 124 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 3 - Forks: 3

RajLabMSSM/echoconda

echoverse module: conda environment handling

Language: R - Size: 551 KB - Last synced at: 11 months ago - Pushed at: 11 months ago - Stars: 1 - Forks: 2

RajLabMSSM/echoLD

echoverse module: LD downloading and processing

Language: R - Size: 1.81 MB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

RajLabMSSM/downloadR

echoverse module: Single- and multi-threaded downloading functions.

Language: R - Size: 357 KB - Last synced at: 12 months ago - Pushed at: 12 months ago - Stars: 0 - Forks: 0

RajLabMSSM/AR_Rotation

Language: HTML - Size: 11.9 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/ldsc

LD Score Regression Pipeline

Language: Python - Size: 6.29 MB - Last synced at: over 1 year ago - Pushed at: almost 2 years ago - Stars: 0 - Forks: 1

RajLabMSSM/devoptera

⏩ Practical tools for R developers :rewind: :wrench::bat: :hammer::bat: :toolbox::bat:

Language: R - Size: 13.2 MB - Last synced at: about 1 year ago - Pushed at: about 1 year ago - Stars: 1 - Forks: 0

RajLabMSSM/echoannot

echoverse module: Annotate fine-mapping results

Language: R - Size: 28.8 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

RajLabMSSM/isoMiGA

The isoform-centric microglia genomic atlas.

Size: 599 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/snakeSV

Snakemake pipeline for SV discovery and analysis

Language: Python - Size: 401 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 4 - Forks: 1

RajLabMSSM/suez-snakemake-pipeline

Snakemake pipeline for calling QTLs using suez

Language: R - Size: 103 MB - Last synced at: over 1 year ago - Pushed at: almost 4 years ago - Stars: 0 - Forks: 0

RajLabMSSM/SGSeq-pipeline Fork of plagnollab/RNASeq_pipeline

snakemake refactoring of legacy code for splicing analysis

Language: R - Size: 11.2 MB - Last synced at: over 1 year ago - Pushed at: about 5 years ago - Stars: 0 - Forks: 0

RajLabMSSM/STMN2-splicing

Analysis of cryptic splicing in the STMN2 locus across the NYGC ALS consortium

Language: Python - Size: 26.2 MB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 1 - Forks: 0

RajLabMSSM/Password-protection-for-static-pages Fork of matteobrusa/Password-protection-for-static-pages

Password protection for static pages

Language: HTML - Size: 61.5 KB - Last synced at: over 1 year ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

RajLabMSSM/EWCE-pipeline

A set of scripts for running Expression-Weighted Cell-type Estimation (EWCE)

Language: R - Size: 26.4 KB - Last synced at: over 1 year ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

RajLabMSSM/scRNAseq-Microglia-Pilot Fork of emilykozik/scRNAseq-Microglia-Pilot

single cell fresh microglia and single nuclei RNA seq

Size: 59.6 MB - Last synced at: almost 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 0

RajLabMSSM/Genotype_QC_Pipeline_2.0

Language: Python - Size: 29.3 KB - Last synced at: almost 2 years ago - Pushed at: about 2 years ago - Stars: 0 - Forks: 0

RajLabMSSM/editing-pipeline

A set of snakemake pipelines for doing RNA editing

Language: R - Size: 767 KB - Last synced at: over 1 year ago - Pushed at: over 2 years ago - Stars: 2 - Forks: 3

RajLabMSSM/echoplot

echoverse module: Locus plot creation for fine-mapping and colocalization studies.

Language: R - Size: 6.86 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 1 - Forks: 0

RajLabMSSM/echoverseTemplate

Self-updating template for creating echoverse R packages.

Language: R - Size: 389 KB - Last synced at: about 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/ggLocusZoom 📦

Create LocusZoom-style plots in R.

Language: R - Size: 36.1 MB - Last synced at: about 2 years ago - Pushed at: about 2 years ago - Stars: 15 - Forks: 4

RajLabMSSM/echolocatoR

Automated statistical and functional fine-mapping pipeline with extensive API access to datasets.

Language: R - Size: 397 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 19 - Forks: 11

RajLabMSSM/PD_omics_review

Data and code associated with the Parkinson's Disease review paper by Schilder, Navarro & Raj (2021).

Language: HTML - Size: 194 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

RajLabMSSM/New_beginnings_2.0

Size: 10.7 KB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 1 - Forks: 1

RajLabMSSM/MiGA_public_release

Language: HTML - Size: 261 MB - Last synced at: over 1 year ago - Pushed at: over 3 years ago - Stars: 6 - Forks: 0

RajLabMSSM/catalogueR

Easy-to-use R wrappers for the eQTL Catalogue's API (both with tabix and the REST API).

Language: R - Size: 105 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 12 - Forks: 1

RajLabMSSM/AMP_AD_StructuralVariation

Repository for the AMP-AD structural variation manuscript

Language: HTML - Size: 333 MB - Last synced at: almost 2 years ago - Pushed at: about 3 years ago - Stars: 4 - Forks: 3

RajLabMSSM/Fine_Mapping_Shiny

Shiny app for plotting and sharing fine-mapping results from echolocatoR

Language: R - Size: 2.31 GB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 1 - Forks: 3

RajLabMSSM/echotabix

echoverse module: Tabix indexing and querying.

Language: R - Size: 1.15 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/Fine_Mapping

Fine mapping of genes associated with Parkinson's Disease using a variety of methods

Language: HTML - Size: 3.17 GB - Last synced at: about 2 years ago - Pushed at: about 3 years ago - Stars: 5 - Forks: 2

RajLabMSSM/echodeps

echoverse module: Create package dependency graphs

Language: R - Size: 227 KB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/echofinemap

echoverse module: Statistical and functional fine-mapping functions.

Language: R - Size: 1.01 MB - Last synced at: about 2 years ago - Pushed at: over 2 years ago - Stars: 0 - Forks: 0

RajLabMSSM/echodata

echoverse module: Example data.

Language: R - Size: 14.2 MB - Last synced at: over 1 year ago - Pushed at: over 1 year ago - Stars: 0 - Forks: 0

RajLabMSSM/summary-gwas-imputation Fork of hakyimlab/summary-gwas-imputation

harmonization, liftover, and imputation of summary statistics from GWAS

Size: 138 KB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

RajLabMSSM/Minerva_Notes

Tutorials, tips and tricks with the Minerva computing cluster

Size: 411 KB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 1 - Forks: 0

RajLabMSSM/MiGASti

Cultured and stimulated human microglial samples

Size: 179 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

RajLabMSSM/MyND-Analysis

MyND Project

Language: HTML - Size: 84.2 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 1 - Forks: 0

RajLabMSSM/PD_scRNAseq

Seurat analysis pipelines for Parkinson's Disease scRNA-seq data from monocytes

Language: HTML - Size: 877 MB - Last synced at: about 2 years ago - Pushed at: about 4 years ago - Stars: 0 - Forks: 0

RajLabMSSM/COVID19_PheWAS

Genetic signatures COVID-19 susceptibility

Language: HTML - Size: 27.4 MB - Last synced at: about 2 years ago - Pushed at: over 3 years ago - Stars: 0 - Forks: 0

RajLabMSSM/DeepSEA

R analyses and plots of DeepSEA (http://deepsea.princeton.edu) output, applied to Alzheimer's disease data.

Language: R - Size: 93.8 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 0 - Forks: 0

RajLabMSSM/Dey_DeepLearning

Searchable, pre-computed, variant-level predictions from several deep learning models.

Size: 0 Bytes - Last synced at: about 2 years ago - Pushed at: over 4 years ago - Stars: 0 - Forks: 0

RajLabMSSM/polyfun Fork of omerwe/polyfun

PolyFun (POLYgenic FUNctionally-informed fine-mapping)

Language: Python - Size: 215 MB - Last synced at: about 2 years ago - Pushed at: almost 5 years ago - Stars: 0 - Forks: 0

RajLabMSSM/Tensor_myeloid

Related scripts and files for the paper "Tensor Decomposition of Stimulated Monocyte and Macrophage Gene Expression Profiles Identifies Neurodegenerative Disease-specific Trans-eQTLs"

Language: Rich Text Format - Size: 48.9 MB - Last synced at: about 2 years ago - Pushed at: over 5 years ago - Stars: 1 - Forks: 0

RajLabMSSM/GTExV6PRareVariation Fork of joed3/GTExV6PRareVariation

Repository to reproduce analyses from the GTEx V6P Rare Variation Manuscript

Language: R - Size: 5.95 MB - Last synced at: almost 2 years ago - Pushed at: over 7 years ago - Stars: 0 - Forks: 0

RajLabMSSM/MOFA Fork of bioFAM/MOFA

Multi-Omics Factor Analysis

Language: R - Size: 115 MB - Last synced at: about 2 years ago - Pushed at: about 6 years ago - Stars: 0 - Forks: 0

RajLabMSSM/qtltools Fork of qtltools/qtltools

A complete tool set for molecular QTL discovery and analysis

Language: C++ - Size: 49.5 MB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

RajLabMSSM/fastqtl Fork of hall-lab/fastqtl

Fork of FastQTL for SVs (to run on Minerva)

Language: C++ - Size: 46.2 MB - Last synced at: almost 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0

RajLabMSSM/gtex-pipeline Fork of broadinstitute/gtex-pipeline

GTEx Consortium data production and analysis pipelines

Language: Python - Size: 205 KB - Last synced at: about 2 years ago - Pushed at: over 6 years ago - Stars: 0 - Forks: 0