BEDApub

besca

BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis

splicekit

splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq

designit

Blocking and randomization for experimental design

space-microbe

GeMS

Gene set management system based on a MongoDB backend

bios-to-go

Static files of the BIOS, aka Bioinfo-C, library

bksnake

Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow

dynamic-form

HBVouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

kinex

Kinex infers causal kinases from phosphoproteomics data

microbiome10XVisium

PMDA-Summer-School

Public website of Roche PMDA Summer School

refsnake

Snakemake workflow to generate reference genomes and annotations

ribiosNGS

Next-generation sequencing data analysis with ribios

metadata-registration-api

A flask microservice to register and manage metadata via an API.

ngs-tools

Helper tools written in C, Bash, Python, and R for next-generation sequencing data analysis.

ribiosGSEA

Functions for gene-set analysis of various kinds supported by ribios

ribiosPlot

Data transformation and visualization with the ribios suite

ribiosScripts

Rscripts as command-line tools from the corresponding repository on BEDA github.

roger

Understand gene expression regulation with ROGER (Roche Omnibus of Gene Expression Regulation)

MelanomaCITResponse_scRNAseq_TILandPBMC_publication

This repository includes notebooks utilized to produce results for the publication "Myeloid-T cell interplay, cell state transitions and checkpoint inhibitor response in melanoma"

BP40087_paper_supplementary_code

Supplementary source code related to the clinical trial BP40087

CD8-immune-phenotype-paper-supplementary

Supplementary source code for the CD8 immune phenotype publication

cd8ippred

R package to predict immune phenotypes from RNA-Seq

GLOC-hep_distr_and_system_param

ribiosAnnotation

Annotate features (genes, mRNAs, proteins, ...) with ribios

ribiosExpression

Data structure and functions for gene expression analysis

ribiosMath

Mathematical objects and functions in the ribios software suite

ribiosUtils

The ribiosUtils package, a swiss-army knife for bioinformatics and computational biology tasks in drug discovery

sapiens

Gene Signature Annotation Pipeline