LabClaw – Operating Layer for LabOS (Stanford-Princeton AI Co-Scientists)

Analysis pipeline for small RNA SLAMseq data

An ebook reader application supporting PDF, DjVu, EPUB, FB2 and many more formats, running on Cervantes, Kindle, Kobo, PocketBook and Android devices

Analysis of the 210 patient cohort processed by the OHSU/PNNL PTRC

AirPlay Unix mirroring server

Workflow to reproduce results and figures for the second BeatAML manuscript

Synthego ICE - Inference of CRISPR Editing software

rapids-singlecell: GPU-accelerated framework for scRNA analysis

Formatting NCI60 data into cosmos ready inputs and generation of testable hypothesis connecting cell-line specific TF and metabolic deregulations.

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

A brief, quick and dirty introduction to Sequence Similarity Networks

A library of free open source icons for science illustrations in biology and chemistry

ShinyProxy - Open Source Enterprise Deployment for Shiny and data science apps

There are tons of electronic lab notebook out there, but only few of them are actually usable. It usually takes months for a scientist to decide which ELN is the right software to go.

A small database of weird gene annotations

Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.

CUT&RUN and CUT&Tag data processing and analysis

Demonstration of user management and authentication system in R Shiny

📓 eLabFTW is the most popular open source electronic lab notebook for research labs.

Shiny App for interactive oligo probe design.

Skip the peaks and expose RNA-binding in CLIP data

NGS-PrimerPlex is a high-throughput tool for mupltiplex primer design

CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either …

Analysis notebooks and data for AML hierarchies paper

Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

TEProf2 Pipeline used to find promoters and predict protein sequences from RNA-sequencing data

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing