BIMSB bioinformatics platform / Akalin Lab

maui

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

ikarus

Identifying tumor cells at the single-cell level using machine learning

netSmooth

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

VoltRon

VoltRon: spatial omic analysis toolbox for multiomic integration using image registration

pigx_rnaseq

Pipeline for RNAseq

swineherd

Let the Shepherd herd Guix System containers

pigx_sars-cov-2

PiGx SARS-CoV-2 wastewater sequencing pipeline

guix-bimsb

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

bavaria

Batch-adversarial variational auto-encoder (BAVARIA) for simultaneous dimensionality reduction and integration of single-cell ATAC-seq datasets

crispr_DART

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

deconvR

The deconvR is an R package designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model.

guix-bimsb-nonfree

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

pigx_chipseq

Pipeline for Analysis of ChIP-Seq data

RCAS

R package for the RNA Centric Annotation System (RCAS)

scmaui

ccfDNA_ACSS_manuscript

The repo for the manuscript "Cardiovascular disease biomarkers derived from circulating cell-free DNA methylation"

mergen

AI-Driven Code Generation, Explanation and Execution for Data Analysis

bimsbbioinfo.github.io

website for the platform

uyar_et_al_multiomics_deeplearning

maui goes pancancer

mergenstudio

rcas-web

Web interface for RCAS

BayesPrism

A Fully Bayesian Inference of Tumor Microenvironment composition and gene expression

collab_rrustemi_selbach_prisma

Data and scripts related to short linear motif analyses for the collaboration with Trendelina Rrustemi from Matthias Selbach's Lab

flexynesis-benchmarks

Comprehensive continuous benchmarking of tools for multi-omics data integration

GEOparse

Python library to access Gene Expression Omnibus Database (GEO)

mergen-manuscript

pigx-common

Common infrastructure used by all PiGx pipelines

rstudio

RStudio is an integrated development environment (IDE) for R

snakemake

This is the development home of the workflow management system Snakemake. For general information, see

tibanna-bimsb

Tibanna helps you run your genomic pipelines on Amazon cloud (AWS). It is used by the 4DN DCIC (4D Nucleome Data Coordination and Integration Center) to process data. Tibanna supports CWL/WDL (w/ docker), Snakemake (w/ conda) and custom Docker/shell command.