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2022-07-shelllessondata

Shell lesson data

besca

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

besca_publication_results

besca_publication_signature_validation

Signature validation for the BESCA publication

bescape

BESCApe is a cell deconvolution package.

bios-to-go

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

bksnake

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

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

complexsim

designit

Blocking and randomization for experimental design

dynamic-form

gems

Gene set management system based on a MongoDB backend

geneocr-api

geneocr-ui

geowizard

GeoWizard

gloc-hep_distr_and_system_param

hbvouroboros

HBVouroboros automates sequencing-based HBV genotyping and expression profiling

kinex

Kinex infers causal kinases from phosphoproteomics data

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"

metadata-registration-api

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

metadata-registration-lib

Library for the metadata-registration tools.

microbiome10xvisium

ngs-tools

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

pd1-il2v_in-vivo_tils_panc02_publication

This repository includes notebooks utilized to produce results for the publication on the PD1-IL2v in vivo PancO2 study (TIL scRNA-seq analysis).

pmda-summer-school

Public website of Roche PMDA Summer School

publication_tyrp1tcb_antipdl1

This repository contains the R scripts to generate 1000 virtual patients, simulate their expected tumor growth profile, and evaluate it using RECIST v1.1, outputting ORR, DoR and PFS

refsnake

Snakemake workflow to generate reference genomes and annotations

ribiosannotation

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