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anaconda

Anaconda turns your Sublime Text 3 in a full featured Python development IDE including autocompletion, code linting, IDE features, autopep8 formating, McCabe complexity checker Vagrant and Docker support for Sublime Text 3 using Jedi, PyFlakes, pep8, MyPy, PyLint, pep257 and McCabe that will never freeze your Sublime Text 3

ashr

An R package for adaptive shrinkage

bivariate_scan

clusterprofiler

:bar_chart:statistical analysis and visualization of functional profiles for genes and gene clusters

coloc2

Upgrade to coloc

cpbayes

CPBayes (Bayesian meta analysis for studying cross-phenotype genetic associations) package

deepsequence

A generative latent variable model for biological sequence families.

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

depict

DEPICT code, instructions and an example

extreme-deconvolution

Density estimation using Gaussian mixtures in the presence of noisy, heterogeneous and incomplete data

flowsom-rtsne-example

Worked example showing how to cluster and visualize flow/mass cytometry data using FlowSOM and Rtsne

focus

FOCUS: Fine-mapping Of CaUsal gene Sets

forestplot

Advanced forest plots in R using grid graphics

fusion_twas

methods for functional summary-based imputation

genesis

GENetic Effect-Size distribution Inference from Summary-level data

gganimate

A Grammar of Animated Graphics

gnova

A principled framework to estimate annotation-stratified genetic covariance using GWAS summary statistics.

gtexresults

Code and data resources accompanying Urbut et al (2017), "Flexible statistical methods for estimating and testing effects in genomic studies with multiple conditions."

hess

Estimate local SNP heritability and genetic covariance from GWAS summary association statistics.

hipo

Heritability Informed Power Optimization (HIPO)

hlmm

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

immuneresistance

This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".

lcv

Software implementing the Latent Causal Variable Model

ldsc

LD Score Regression (LDSC)

limix

Linear mixed model for genomic analyses.

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mashr

An R package for multivariate adaptive shrinkage.

mendelianrandomization

:exclamation: This is a read-only mirror of the CRAN R package repository. MendelianRandomization — Mendelian Randomization Package