AndrasHartmann

markdown-here

Google Chrome, Firefox, and Thunderbird extension that lets you write email in Markdown and render it before sending.

zotero

Zotero is a free, easy-to-use tool to help you collect, organize, annotate, cite, and share your research sources.

python-mode

Vim python-mode. PyLint, Rope, Pydoc, breakpoints from box.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

substance

A JavaScript library for web-based content editing.

FreeML

A List of Data Science/Machine Learning Resources (Mostly Free)

texture

A visual editor for research.

ojs

Open Journal Systems is open source software to manage scholarly journals.

renjin

JVM-based interpreter for the R language for the statistical analysis.

rootstock

Clone me to create your Manubot manuscript

scanorama

Panoramic stitching of single cell data

conos

R package for the joint analysis of multiple single-cell RNA-seq datasets

velocyto.R

RNA velocity estimation in R

zot_bib_web

Create interactive web bibliographies based on Zotero collections

philentropy

Information Theory and Distance Quantification with R

LogicNG

The Next Generation Logic Library

rsession

R sessions wrapping for Java

recount

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/

deepcpg

Deep neural networks for predicting CpG methylation

geneSynonym

Quick access to gene synonyms

sc-rna-seq-pipeline

bioLQM

toolkit for the manipulation and analysis of Logical Qualitative Models of biological regulatory networks

shiny-loadbalancer

Shiny App for Load Balancing

caspo-ts

RefBool

RefBool - a reference-based algorithm for booleanizing gene expression data

cocabu

harissa

Tools for mechanistic gene network inference from single-cell data

BGFit

Web application that manages experimental data from lab and performs data-modeling

rgurobi

Solve optimisation problems using the commercial Gurobi software package

caspots

Boolean network inference from time series data with perturbations