170 Open source projects that are alternatives of or similar to IsoQuant

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

An automated RNA-seq pipeline using Nextflow

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

An accurate and ultra-fast hybrid genome assembler

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

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

TransPi – a comprehensive TRanscriptome ANalysiS PIpeline for de novo transcriptome assembly

Long read / genome alignment software

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

Predict plasmids from uncorrected long read data

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

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

A versatile sequenced read processor for nanopore direct RNA sequencing

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

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

No description or website provided.

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

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

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

🐳 Bio-dockers: dockerized bioinformatic tools

Whole Exome/Whole Genome Sequencing alignment pipeline

GREIN : GEO RNA-seq Experiments Interactive Navigator

Differential expression analysis for single-cell RNA-seq data.

Code pipeline for the PaccMann^RL in iScience: https://www.cell.com/iscience/fulltext/S2589-0042(21)00237-6

Tools and software library developed by the ONT Applications group

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

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

Efficient handling of FASTQ files from Python

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

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

A scalable bacterial genome assembly, annotation and analysis pipeline

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Multiome GRN inference.

A small python program to simulate a real-time Nanopore sequencing run based on a previous experiment.

myVCF: a web-based platform for target and exome mutations data management

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

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

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

Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.

🐍 Snakefiles for common RNA-seq data analysis workflows.

Nanopore demultiplexing, QC and alignment pipeline

SARS-CoV-2 workflow for nanopore sequence data

Faster BWA-MEM2 using learned-index

Differential Gene Correlation Analysis

A library for manipulating bioinformatics sequencing formats in Apache Spark

🔬 De novo assembly of nanopore reads using nextflow

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

A proof of concept RNA-Seq pipeline with Nextflow

Minor Variant Calling and Phasing Tools

CWL tools and workflows for GGR

Exome/Capture/RNASeq Pipeline Implementation using snakemake

A prediction model for differential gene expression (DE) based on genome-wide regulatory interactions

List of IARC bioinformatics nextflow pipelines

Utilities for analyzing next generation sequencing data.

Multi-sample somatic variant caller