BIMSBbioinfo/compgen2018

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BIMSBbioinfo/compgen2018

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teaching material for compgen2018 course

janggu

Deep learning infrastructure for genomics

Jupyter Notebook

compgen2021

genomation

R package for genomic feature analysis and visualization

maui

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

Jupyter Notebook

VoltRon

Spatial omic analysis toolbox for multi-resolution and multi-omic integration using image registration

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

intro2UnixandSGE

resource for unix and SGE beginners

pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline

flexynesis

A deep-learning based multi-modal data integration suite that aims to achieve synesis in a flexible manner

pigx

Pipelines in genomics

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

Jupyter Notebook

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

HOT regions paper

mergen

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

pigx_bsseq

bisulfite sequencing pipeline from fastq to methylation reports

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.

ciRcus

An R package for annotation of circular RNAs

pigx_scrnaseq

Pipeline for analysis of Dropseq single cell data

guix-bimsb-nonfree

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

crispr_DART

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

projectTemplate

Strategies_for_analyzing_BS-seq

SingleCell_2018

Repository for Single Cell Analysis Course in MDC

scmaui

Jupyter Notebook

pigx_chipseq

Pipeline for Analysis of ChIP-Seq data

ikarus---auxiliary

Jupyter Notebook

scbrowse

An interactive browser for single-cell ATAC-seq data

RCAS

R package for the RNA Centric Annotation System (RCAS)

ccfDNA_ACSS_manuscript

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

slimR

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

pigx_docs

Documentation for PiGx

guix.install

Install (and import) R packages with Guix from within your R session

scregseg

Single-cell regulatory landscape segmentation

Jupyter Notebook

htd3

visualisation library for genetic data based on d3.js

uyar_et_al_multiomics_deeplearning

maui goes pancancer

mergenstudio

scipipeline

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

puppet-bimsb-guix

Puppet module for deploying Guix

sudo

bimsbbioinfo.github.io

website for the platform

multiomics_vs_panelseq

The repo of the "Multi-omics alleviates the limitations of panel-sequencing for cancer drug response prediction" manuscript

reg2gene

flexynesis-benchmarks

Comprehensive continuous benchmarking of tools for multi-omics data integration

RCAS_meta-analysis

The repo is to host the scripts and the results of multiple RBPs.

rcas-web

Web interface for RCAS

scmaui-experiments

Tutorials for scMaui

Jupyter Notebook

froehlich_uyar_et_al_2020

MyoExplorer

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

compgen2015material

makeNGSnake

spatialNetSmooth

ZarrArray

Zarr backend for DelayedArray objects