145 Open source projects that are alternatives of or similar to alevin-fry

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

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

Manuscript for functional prediction of transcriptomic “dark matter” across species

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

Multiome GRN inference.

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

Dynamical systems methods for RNA velocity analysis

Reference-based transcript discovery from long RNA read

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

Next-Gen Sequencing tools from the Horvath Lab

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

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

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

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

Single cell analysis in the browser

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

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

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

Deep Learning based cell composition analysis with Scaden.

A tool that allows to get UMI counts from a single cell protein assay

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

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

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

Pipeline for annotating genomes using long read transcriptomics data with pinfish

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

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

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

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

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

Digital Cell Sorter (DCS): single cell RNA-seq analysis toolkit. Documentation:

🐍 Snakefiles for common RNA-seq data analysis workflows.

Discrete Distributional Differential Expression

scLearn：Learning for single cell assignment

Pruning and quantization for SSD. Model compression.

💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format

RNA-seq analysis pipeline for detection gene-fusions

R API and htmlwidget for Vitessce

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

Single-cell exploratory data analysis for RNA-Seq

spatial transcriptome, single cell

Summer school course materials collection

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

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

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

CWL tools and workflows for GGR

An R implementation of the SINCERA pipeline for single cell RNA-seq profiling analysis

No description or website provided.

Interactive Differential Expression AnaLysis - DE made accessible and reproducible

scisorseqr is an R-package for processing of single-cell long read data and analyzing differential isoform expression across any two conditions

A pipeline for the computational evaluation of RNA-Seq data

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

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

FEELnc : FlExible Extraction of LncRNA

Metacell - Single-cell mRNA Analysis

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

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

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

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

GREIN : GEO RNA-seq Experiments Interactive Navigator