BIMSB bioinformatics platform

Repositories

janggu

Deep learning infrastructure for bioinformatics

machine-learning bioinformatics deep-learning genomics epigenetics

Jupyter Notebook GPL-3.0 12 140 0 0 Updated Aug 4, 2020

pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

bioinformatics snakemake pipeline guix reproducibility

Python GPL-3.0 3 3 24 1 Updated Aug 3, 2020

scregseg

Single-cell regulatory landscape segmentation

Python GPL-3.0 0 0 0 0 Updated Jul 31, 2020

crispr_DART

A workflow to analyse sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data

python r rmarkdown bioconductor crispr-analysis crispr indels

Python GPL-3.0 0 1 0 0 Updated Jul 31, 2020

froehlich_uyar_et_al_2020

R 0 1 0 0 Updated Jul 30, 2020

maui

Multi-omics Autoencoder Integration: Deep learning-based heterogenous data analysis toolkit

bioinformatics deep-learning cancer-genomics autoencoder multi-omics latent-factor-model

Jupyter Notebook GPL-3.0 5 26 4 0 Updated Jul 28, 2020

pigx_rnaseq

Pipeline for RNAseq

snakemake pipeline rnaseq guix reproducibility

Python GPL-3.0 8 13 30 0 Updated Jul 24, 2020

pigx_scrnaseq

Pipeline for analysis of Dropseq single cell data

guix snakemake-workflows dropseq single-cell-rna-seq

Python 5 7 25 1 Updated Jul 20, 2020

compgen

1 0 0 0 Updated Jul 15, 2020

MyoExplorer

Companion code for: Kim et. al., Single-nucleus transcriptomics reveals functional compartmentalization in syncytial skeletal muscle cells

HTML 0 0 0 0 Updated Jul 13, 2020

guix-bimsb-nonfree

GNU Guix package definitions for proprietary software, or software with unclear licenses.

scheme bioinformatics hpc guix package-management gnu-guix

Scheme GPL-3.0 2 5 0 0 Updated Jun 27, 2020

guix-bimsb

Packages for GNU Guix that have not yet or will not be submitted upstream for various reasons

scheme bioinformatics hpc guix package-management gnu-guix

Scheme GPL-3.0 4 10 0 0 Updated Jun 27, 2020

bimsbbioinfo.github.io

website for the platform

HTML 8 1 0 2 Updated Jun 21, 2020

pigx_docs

Documentation for PiGx

documentation bioinformatics pipelines reproducibility pigx

1 3 0 0 Updated Jun 8, 2020

deep-seq-workflow

Deep Seq experiments backup workflow

Ruby MIT 0 0 2 1 Updated May 7, 2020

RCAS

R package for the RNA Centric Annotation System (RCAS)

go reporting bioconductor rna interactive-plots msigdb modification

R 3 3 2 0 Updated May 5, 2020

pigx

Pipelines in genomics

snakemake genomics rnaseq guix dropseq bisulfite-sequencing chipseq

Python GPL-3.0 4 6 10 0 Updated Apr 6, 2020

ciRcus

An R package for annotation of circular RNAs

R 6 8 11 (2 issues need help) 3 Updated Mar 30, 2020

pigx_chipseq

Pipeline for Analysis of ChIP-Seq data

snakemake pipeline guix reproducibility chipseq

Python GPL-3.0 7 3 46 0 Updated Mar 25, 2020

genomation

R package for genomic feature analysis and visualization

R 21 49 23 0 Updated Mar 6, 2020

FastQC

Forked from s-andrews/FastQC

A quality control analysis tool for high throughput sequencing data

Java 33 0 0 0 Updated Feb 28, 2020

rbc_docs

Forked from bgruening/rbc_docs

RBC de.NBI documents

4 0 0 0 Updated Feb 10, 2020

netSmooth

netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation

bioinformatics genomics single-cell

R 6 19 4 0 Updated Dec 16, 2019

scipipeline

Snakemake pipeline for processing single-cell combinatorial indexing ATAC seq data

Python 0 2 0 0 Updated Oct 7, 2019

HOT-or-not-examining-the-basis-of-high-occupancy-target-regions

HOT regions paper

R 0 8 0 0 Updated Jun 18, 2019

Muthel_et_al_lin53_2019

Reproduce bioinformatics analysis for the manuscript: Muthel et al, 2019.

HTML 0 0 0 0 Updated May 9, 2019

rcas-web

Web interface for RCAS

JavaScript AGPL-3.0 0 1 0 0 Updated Feb 8, 2019

slimR

Short Linear Motif (SLiM) Analysis in the context of human diseases

mutations polymorphism uniprot clinvar protein-protein-interaction short-linear-motifs disease-causing-mutations

R 2 2 0 0 Updated Dec 11, 2018

bioconda-recipes

Forked from bioconda/bioconda-recipes

Conda recipes for the bioconda channel.

Shell 1,536 0 0 0 Updated Dec 10, 2018

collab_meyer_selbach_glut1

Reproduce bioinformatics analysis for the paper Meyer, K. et al., Cell, 2018.

r protein-interaction polymorphism clinvar peptides protein-disorder short-linear-motifs

0 0 0 0 Updated Nov 21, 2018