Alternatives and similar repositories for alevin-fry

Users that are interested in alevin-fry are comparing it to the libraries listed below

• 10XGenomics / vartrix
  Single-Cell Genotyping Tool
  ☆214Updated 2 years ago
• 10XGenomics / bamtofastq
  Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
  ☆66Updated 3 weeks ago
• hbc / knowledgebase
  recipes that save time
  ☆145Updated 3 months ago
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆155Updated last month
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆167Updated 2 weeks ago
• pachterlab / seqspec
  machine-readable file format for genomic library sequence and structure
  ☆125Updated 3 months ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆112Updated last month
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆181Updated last month
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆207Updated 2 months ago
• 10XGenomics / subset-bam
  ☆82Updated last year
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆107Updated 6 months ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆122Updated 2 months ago
• broadinstitute / ABC-Enhancer-Gene-Prediction
  Cell type specific enhancer-gene predictions using ABC model (Fulco, Nasser et al, Nature Genetics 2019)
  ☆241Updated 5 months ago
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆190Updated 3 weeks ago
• BUStools / bustools
  Tools for working with BUS files
  ☆102Updated 6 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆242Updated last week
• singleron-RD / CeleScope
  Single Cell Analysis Pipelines
  ☆112Updated last week
• timoast / sinto
  Tools for single-cell data processing
  ☆128Updated last year
• nf-core / rnafusion
  RNA-seq analysis pipeline for detection of gene-fusions
  ☆166Updated 2 weeks ago
• jackh726 / bigtools
  A high-performance BigWig and BigBed library in Rust
  ☆107Updated last month
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆109Updated 10 months ago
• vaquerizaslab / fanc
  FAN-C: Framework for the ANalysis of C-like data
  ☆120Updated last year
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆79Updated 2 weeks ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆118Updated 2 years ago
• AlexandrovLab / SigProfilerExtractor
  SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the n…
  ☆168Updated 3 weeks ago
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆122Updated last week
• open2c / distiller-nf
  A modular Hi-C mapping pipeline
  ☆100Updated last year
• dohlee / metheor
  Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
  ☆48Updated 3 months ago
• Teichlab / tracer
  TraCeR - reconstruction of T cell receptor sequences from single-cell RNAseq data
  ☆132Updated 2 years ago