107 Open source projects that are alternatives of or similar to NGS

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

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

Single cell analysis in the browser

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

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

Dynamical systems methods for RNA velocity analysis

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

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

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

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

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

Reference-based transcript discovery from long RNA read

Feature extraction algorithm for genomic data

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

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

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

CWL tools and workflows for GGR

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

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

Software for exploration of gene expression data from single-cell RNA sequencing.

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

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

GREIN : GEO RNA-seq Experiments Interactive Navigator

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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

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

Nextflow RNA-Seq Best Practice analysis pipeline, used at the SciLifeLab National Genomics Infrastructure.

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

A pipeline for the computational evaluation of RNA-Seq data

CellNet: network biology applied to stem cell engineering

A proof of concept RNA-Seq pipeline with Nextflow

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

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

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

🐍 Snakefiles for common RNA-seq data analysis workflows.

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

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

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

RNASeq pipeline

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches

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

FEELnc : FlExible Extraction of LncRNA

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Scripts to import your FeatureCounts output into DEXSeq

Differential Gene Correlation Analysis

Porting DESeq2 and DEXSeq into python via rpy2

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

R package to do the Ligand Receptor Analysis Visualization

Fast and accurate gene fusion detection from RNA-Seq data

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

RNA-seq analysis pipeline for detection gene-fusions

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

An automated RNA-seq pipeline using Nextflow

Simulating single-cell data using gene regulatory networks 📠

Fast visualization tool for large-scale and high dimensional single-cell data

Clone identification from single-cell data

Version 2.1.0 released

Summer school course materials collection