112 Open source projects that are alternatives of or similar to cellSNP

Efficient genotyping bi-allelic SNPs on single cells

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

Dynamical systems methods for RNA velocity analysis

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

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

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.

Next-Gen Sequencing tools from the Horvath Lab

Single cell analysis in the browser

Multiome GRN inference.

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

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

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

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

🐍 Snakefiles for common RNA-seq data analysis workflows.

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

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

Porting DESeq2 and DEXSeq into python via rpy2

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

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

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

echt rapid variant annotation and filtering

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

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

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

mgatk: mitochondrial genome analysis toolkit

spatial transcriptome, single cell

A tool for semi-automatic cell type annotation

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

FEELnc : FlExible Extraction of LncRNA

R API and htmlwidget for Vitessce

Papers with code for single cell related papers

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

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

CWL tools and workflows for GGR

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

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

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

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

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

A fast, accurate, and modularized dimensionality reduction approach based on diffusion harmonics and graph layouts. Escalates to millions of samples on a personal laptop. Adds high-dimensional big data intrinsic structure to your clustering and data visualization workflow.

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

RNA-seq analysis pipeline for detection gene-fusions

No description or website provided.

Summer school course materials collection

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

Feature extraction algorithm for genomic data

Reference-based transcript discovery from long RNA read

Pipeline for annotating genomes using long read transcriptomics data with pinfish

Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

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

Streamlining SLAM-seq analysis with ultra-high sensitivity

A pipeline for the computational evaluation of RNA-Seq data

Differential Gene Correlation Analysis

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

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

Version 2.1.0 released