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10x_vs_bd_dropout

algorithm-optimization-project-machine-learning

alpine_workshop

basic rutine to build docker images from alpine base img

atlas_protocol

A computational protocol for atlas-level data integration and analysis as performed in Salcher et al. (2022).

crc_atlas_neutro

Scripts required for the DE and velocity analysis of the MUI dataset

crc_atlas_velocyto

A nextflow pipeline to run velocyto on 10X/BD samples (CRC atlas project)

current-topics-bioinformatics-lecture

git_training

basic git routines for students

hlaii_typing_tools

A Python API to run HLA II typing tools

infercnvpy

Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.

luca

Single-cell Lung Cancer Atlas with 1.2M cells

machine-learning-content

neofuse

NeoFuse is a user-friendly pipeline for the prediction of fusion neoantigens from tumor RNA-seq data.

neofuse2

NeoFuse2 - A NextFlow based NeoFuse version with support for HLA II

next-preprocesshisto

nextneopi

nextNEOpi: a comprehensive pipeline for computational neoantigen prediction

nextpyrad

Nextflow pipeline to extract features from imaging dataset using Pyradiomics

pca_fibroblast_project

pytorch-tutorial

PyTorch Tutorial for Deep Learning Researchers

random_forest_project

rna-seq-qtl

Workflow for Integration of RNAseq and QTL Analyses in Collaborative Cross Mice

scirpy

A scanpy extension to analyse single-cell TCR and BCR data.

scrnaseq

A single-cell RNAseq pipeline for 10X genomics data

spatial

Templates for spatial transcriptomics data analysis

tesla_gamestop_stock_data