286 Open source projects that are alternatives of or similar to rnaseq-nf

viGEN - A bioinformatics pipeline for the exploration of viral RNA in human NGS data

Analysing Capture Seq Count Data

Transcripts annotation and GO enrichment Fisher tests

Bioinformatic Analysis pipeLine for SomAtic Mutations In Cancer

A library for manipulating bioinformatics sequencing formats in Apache Spark

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

Nextflow basic tutorial for newbie users

Tools for analyzing 10X Genomics data

A proof of concept RNA-Seq pipeline with Nextflow

Multilocus sequence typing by blast using the schemes from PubMLST

Bead-based single-cell atac processing

TAD calling, phase imputation, 3D modeling and more for diploid single-cell Hi-C (Dip-C) and general Hi-C

A fast, scalable, and accurate local ancestry method.

Import and summarize transcript-level estimates for gene-level analysis

Grammar of Scalable Linked Interactive Nucleotide Graphics

Bioconductor package for management of multi-assay data

PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.

Big Compute Learning Labs

Learn interpretable computational phenotyping models from k-merized genomic data

Forward-time simulation in Python using fwdpp

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

phenol: Phenotype ontology library

MindTheGap is a SV caller for short read sequencing data dedicated to insertion variants (all sizes and types). It can also be used as a local assembly tool.

A fast tool for hybrid genome assembly of long and short reads

🐳 Bio-dockers: dockerized bioinformatic tools

Examples to get started with IBM Functional Genomics Platform

Identify phage regions in bacterial genomes for masking purposes

find large indels (in the blind spot between GATK/freebayes and SV callers)

Spark VCF data source implementation for Dataframes

Interactive assembly and analysis of RAD-seq data sets

WebAssembly modules for genomics

A tool to plot significant regions of GWAS

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

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes.

Digital Expression Explorer 2 (DEE2): a repository of uniformly processed RNA-seq data

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

An R framework for phylostratigraphy

Python-based UCSC genome browser snapshot-taker and gallery-maker

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or lost.

Improve the quality of a denovo assembly by scaffolding and gap filling

Command line utility for manipulating Illumina-generated FastQ files.

Explore rearrangements and copy-number amplifications in a cancer genome

A package for designing activity-informed nucleic acid diagnostics for viruses.

Modeling and correcting fragment sequence bias for RNA-seq

pythonic wrapper for libhts (moved to: https://github.com/quinlan-lab/hts-python)

Exome/Capture/RNASeq Pipeline Implementation using snakemake

mgatk: mitochondrial genome analysis toolkit

Explore gnomAD datasets on the web

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

Ultrafast sequence typing and gene detection from NGS raw reads

Predict AMPs in (meta)genomes and peptides

Manhattan plot Generator

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Monorepo with JBrowse 2 web, JBrowse 2 desktop, the JB core package, and core plugins. To customize behaviors, write an in-house plugin.

A pipeline to select optimal markers for microbial phylogenomics and species tree estimation using coalescent and concatenation approaches

Assemblytics is a bioinformatics tool to detect and analyze structural variants from a genome assembly by comparing it to a reference genome.