BEDApub
Roche Pharma Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd, Grenzacherstrasse 124, 4070 Basel
Pinned Repositories
besca
BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
besca_publication_results
bescape
BESCApe is a cell deconvolution package.
bios-to-go
Static files of the BIOS, aka Bioinfo-C, library
designit
Blocking and randomization for experimental design
GeMS
Gene set management system based on a MongoDB backend
kinex
Kinex infers causal kinases from phosphoproteomics data
microbiome10XVisium
space-microbe
splicekit
splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
BEDApub's Repositories
bedapub/besca
BESCA (Beyond Single Cell Analysis) offers python functions for single-cell analysis
bedapub/splicekit
splicekit: an integrative toolkit for splicing analysis from short-read RNA-seq
bedapub/designit
Blocking and randomization for experimental design
bedapub/space-microbe
bedapub/GeMS
Gene set management system based on a MongoDB backend
bedapub/bios-to-go
Static files of the BIOS, aka Bioinfo-C, library
bedapub/bksnake
Public version of bksnake - biokit snakemake - bulk RNASeq Snakemake workflow
bedapub/dynamic-form
bedapub/HBVouroboros
HBVouroboros automates sequencing-based HBV genotyping and expression profiling
bedapub/kinex
Kinex infers causal kinases from phosphoproteomics data
bedapub/microbiome10XVisium
bedapub/PMDA-Summer-School
Public website of Roche PMDA Summer School
bedapub/refsnake
Snakemake workflow to generate reference genomes and annotations
bedapub/ribiosNGS
Next-generation sequencing data analysis with ribios
bedapub/metadata-registration-api
A flask microservice to register and manage metadata via an API.
bedapub/ngs-tools
Helper tools written in C, Bash, Python, and R for next-generation sequencing data analysis.
bedapub/ribiosGSEA
Functions for gene-set analysis of various kinds supported by ribios
bedapub/ribiosPlot
Data transformation and visualization with the ribios suite
bedapub/ribiosScripts
Rscripts as command-line tools from the corresponding repository on BEDA github.
bedapub/roger
Understand gene expression regulation with ROGER (Roche Omnibus of Gene Expression Regulation)
bedapub/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"
bedapub/BP40087_paper_supplementary_code
Supplementary source code related to the clinical trial BP40087
bedapub/CD8-immune-phenotype-paper-supplementary
Supplementary source code for the CD8 immune phenotype publication
bedapub/cd8ippred
R package to predict immune phenotypes from RNA-Seq
bedapub/GLOC-hep_distr_and_system_param
bedapub/ribiosAnnotation
Annotate features (genes, mRNAs, proteins, ...) with ribios
bedapub/ribiosExpression
Data structure and functions for gene expression analysis
bedapub/ribiosMath
Mathematical objects and functions in the ribios software suite
bedapub/ribiosUtils
The ribiosUtils package, a swiss-army knife for bioinformatics and computational biology tasks in drug discovery
bedapub/sapiens
Gene Signature Annotation Pipeline