192 Open source projects that are alternatives of or similar to scCATCH

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

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

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

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

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

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

Multiome GRN inference.

Pipeline for annotating genomes using long read transcriptomics data with pinfish

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

Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.

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

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

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

Next-Gen Sequencing tools from the Horvath Lab

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

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

RNASeq pipeline

Single cell analysis in the browser

Dynamical systems methods for RNA velocity analysis

Reference-based transcript discovery from long RNA read

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

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

scRNA-seq data visualization from scrattch

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Tools for single-cell data processing

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

CUT&RUN and CUT&Tag data processing and analysis

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

Efficient genotyping bi-allelic SNPs on single cells

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

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

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

Fast and accurate gene fusion detection from RNA-Seq data

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

Framework for Metastatic And Clonal History INtegrative Analysis

Scripts to import your FeatureCounts output into DEXSeq

Differential Gene Correlation Analysis

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

Convert between AnnData and SingleCellExperiment

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

gargammel is an ancient DNA simulator

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

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

Mouse cell atlas

An automated RNA-seq pipeline using Nextflow

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

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

MERlin is an extensible analysis pipeline applied to decoding MERFISH data

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

📊 Graphical User Interface for TCC package

R package to visualize gene expression data based on weighted kernel density estimation

Cloud-based single-cell copy-number variation analysis tool

COSMOS (Causal Oriented Search of Multi-Omic Space) is a method that integrates phosphoproteomics, transcriptomics, and metabolomics data sets.

Finds SNP sites from a multi-FASTA alignment file

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

Graph-linked unified embedding for single-cell multi-omics data integration

A guide to using a Seurat object in conjunction with RNA Velocity

Multi-omics analysis protocols by Lyu.

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