107 Open source projects that are alternatives of or similar to Rna Seq Star Deseq2

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

Transposon Insertion Finder - Detection of new insertions in NGS data

DNAscan is a fast and efficient bioinformatics pipeline that allows for the analysis of DNA Next Generation sequencing data, requiring very little computational effort and memory usage.

is an open-source LIMS (laboratory Information Management System) for Next Generation Sequencing sample management, statistics and reports, and bioinformatics analysis service management.

Future Gadget Machine

HTS-compatible wrapper for IgBlast V-(D)-J mapping tool

Reproducible Data Science in Python (SciPy 2019 Tutorial)

VisTrails is an open-source data analysis and visualization tool. It provides a comprehensive provenance infrastructure that maintains detailed history information about the steps followed and data derived in the course of an exploratory task: VisTrails maintains provenance of data products, of the computational processes that derive these products and their executions.

Data intensive science for everyone.

A package for designing compact and comprehensive capture probe sets.

A set of command line tools based on R and JavaScript.

Java utilities for Bioinformatics

SEER, reimplemented in python 🐍🔮

Software Papers as Software Modules: Towards a Culture of Reusable Results

Sequana: a set of Snakemake NGS pipelines

Project metadata manager for PEPs in Python

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

UGENE is free open-source cross-platform bioinformatics software

Method to optimally select samples for validation and resequencing

A robust model for quantitative comparison of ChIP-Seq data sets.

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Dockerised Next Generation Sequencing Pipeline (QC, Align, Calling, Annotation)

rrtools: Tools for Writing Reproducible Research in R

Pathogen-Host Analysis Tool - A modern Next-Generation Sequencing (NGS) analysis platform

Reference-based transcript discovery from long RNA read

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

ABRA2

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

A curated list of reproducible research case studies, projects, tutorials, and media

A simplified pipeline for ctDNA sequencing data analysis

Official code repository for GATK versions 4 and up

Open Source Photometric classification https://supernnova.readthedocs.io

NGLess: NGS with less work

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

Source code for the CERN Analysis Preservation portal

Examples and demos for ReproZip

A DSL for data-driven computational pipelines

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Estimation of per-individual inbreeding coefficients under a probabilistic framework

(No maintenance) OpenGene, core libraries for NGS data analysis and bioinformatics in Julia

R package for analyzing single-cell RNA-seq data

🔬 Empirical CLI

(No maintenance) Detect gene fusion directly from raw fastq files

Papers with code for single cell related papers

dcmjs is a javascript cross-compile of dcmtk (dcmtk.org).

An NGS read trimming tool that is specific, sensitive, and speedy. (production)

Estimation of pairwise distances under a probabilistic framework

MTBseq is an automated pipeline for mapping, variant calling and detection of resistance mediating and phylogenetic variants from illumina whole genome sequence data of Mycobacterium tuberculosis complex isolates.

Everware is about re-useable science, it allows people to jump right in to your research code.

NOTE: This repo is archived. Please see https://github.com/benmarwick/rrtools for my current approach

C library for high-throughput sequencing data formats

A simple tool to calculate reads number and total base count in FASTQ file

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like matrices), normalize and correct interaction matrices, identify and compare the so-called Topologically Associating Domains (TADs), build 3D models from the interaction matrices, and finally, extract structural properties from the models. TADbit is complemented by TADkit for visualizing 3D models

List of IARC bioinformatics nextflow pipelines

Tools to process and analyze deep sequencing data.

🐳 Containerize R Markdown documents for continuous reproducibility

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

A method for variant graph genotyping based on exact alignment of k-mers