95 Open source projects that are alternatives of or similar to GGR-cwl

Multi-omics analysis protocols by Lyu.

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

A graphical user interface for distributed data processing of high throughput genomics

AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

chromatin Variability Across Regions (of the genome!)

Reproducible reanalysis of a combined ChIP-Seq & RNA-Seq data set

Summer school course materials collection

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

HMMRATAC peak caller for ATAC-seq data

🐛 How to use CENTIPEDE to determine if a transcription factor is bound.

Fast in-silico normalization algorithm for NGS data

Analysing Capture Seq Count Data

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

Method for Identifying Novel Transcripts and Isoforms using Equivalence classes, in cancer and rare disease.

CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology

🚦 Run Picard on BAM files and collate 90 metrics into one file.

Lightweight and Fast; RNA-seq quantification at the event-level

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Scripts to import your FeatureCounts output into DEXSeq

Version 2.1.0 released

Feature extraction algorithm for genomic data

Single cell analysis in the browser

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

A versatile sequenced read processor for nanopore direct RNA sequencing

Our VM/Docker sharing infrastructure and management component

Next-Gen Sequencing tools from the Horvath Lab

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Reproducible bioinformatics pipelines in python. Import any Unix tool/command in python.

Differential Gene Correlation Analysis

📊 Graphical User Interface for TCC package

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

CellNet: network biology applied to stem cell engineering

[Experimental] Workflow Definition Language (WDL) to CWL

RNASeq pipeline

CICERO: a versatile method for detecting complex and diverse driver fusions using cancer RNA sequencing data.

Dynamical systems methods for RNA velocity analysis

Fast and accurate gene fusion detection from RNA-Seq data

Pileup biallelic SNPs from single-cell and bulk RNA-seq data

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

CoNekT (short for Co-expression Network Toolkit) is a platform to browse co-expression data and enable cross-species comparisons.

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.

🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.

Processing of single cell RNAseq data for the recovery of TCRs in python

Software for measuring poly(A) tail length and 3′-end modifications using a high-throughput sequencer

An automated RNA-seq pipeline using Nextflow

Streamlining SLAM-seq analysis with ultra-high sensitivity

GREIN : GEO RNA-seq Experiments Interactive Navigator

FEELnc : FlExible Extraction of LncRNA

Deep Learning based cell composition analysis with Scaden.

Porting DESeq2 and DEXSeq into python via rpy2

APIs for discovering genomics tools, their metadata and their containers

SQUID detects both fusion-gene and non-fusion-gene structural variations from RNA-seq data

A course on Analysing Next Generation (/High Throughput etc..) Sequencing data using Bioconductor

A tool to identify, orient, trim and rescue full length cDNA reads

[Alpha] Janis: an open source tool to machine generate type-safe CWL and WDL workflows

Bioinformatics workflows developed for and used on the St. Jude Cloud project.

A proof of concept RNA-Seq pipeline with Nextflow