slowkow

snakefiles

:snake: Snakefiles for common RNA-seq data analysis workflows (STAR and Kallisto).

pytabix

:card_index: Retrieve data in genomic intervals with a Python interface for tabix.

picardmetrics

:vertical_traffic_light: Run Picard on BAM files and collate 90 metrics into one file.

CENTIPEDE.tutorial

:bug: How to use CENTIPEDE to determine if a transcription factor is bound.

homerkit

Read HOMER motif analysis output in R.

circles

:rainbow:

xlmhg

:chart_with_downwards_trend: Non-parametric rank enrichment test for binary data.

highcharter

R wrapper for highcharts based on htmlwidgets

MERmaid

WebGL-based viewer for MERFISH data

AppScanGEO

Source code for ScanGEO Shiny App

btcd

An alternative full node bitcoin implementation written in Go (golang)

CorShrink

R package for adaptive correlation and covariance matrix shrinkage.

DDRTree

An R implementation of the DDRTree algorithm for learning principal graphs

edge

R package for identifying differentially expressed genes from genome-wide gene expression profiling studies.

gallery

Gallery of ggplot2 extensions

hexbin

community curated list of hexagon logos

iSEE

R/shiny interface for interactive visualization of data in objects derived from the SummarizedExperiment class

laravel-user-verification

PHP package built for Laravel 5.* to easily handle a user verification and validate the e-mail

leafcutter

LeafCutter: Annotation-free quantification of RNA splicing. Yang I Li, David A Knowles, Jonathan K Pritchard.

loomR

An R-based interface for loom files

markdown-cv

a simple template to write your CV in a readable markdown file and use CSS to publish/print it.

ncvreg

Regularization paths for SCAD- and MCP-penalized regression models

pagoda2

pycli

:computer: Basic structure for a simple Python CLI

scclust-R

Size-constrained Clustering in R

scde

statistical methods for analyzing single-cell RNA-seq data

seoul256.vim

:deciduous_tree: Low-contrast Vim color scheme based on Seoul Colors

SIMLR

Single-cell Interpretation via Multi-kernel Learning (R code in master branch, Matlab code in matlab branch), implementations of the method published in http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4207.html. Also see http://biorxiv.org/content/early/2017/03/21/118901 for a description of the software.

ubit2

Useful Bioinformatics Tools and Techniques - under construction

xlmhg-js

Javascript implementation of "XL-mHG: A Semiparametric Test for Enrichment in Ranked Lists"