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
  ☆211Updated 2 years ago
• 10XGenomics / bamtofastq
  Convert 10x BAM files to the original FASTQs compatible with 10x pipelines
  ☆66Updated last week
• pachterlab / seqspec
  machine-readable file format for genomic library sequence and structure
  ☆123Updated last month
• pachterlab / kallistobustools
  kallisto | bustools workflow for pre-processing single-cell RNA-seq data
  ☆118Updated 3 years ago
• CostaLab / reg-gen
  Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.
  ☆112Updated 10 months ago
• hbc / knowledgebase
  recipes that save time
  ☆142Updated last month
• pachterlab / kb_python
  A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
  ☆171Updated 4 months ago
• single-cell-genetics / cellsnp-lite
  Efficient genotyping bi-allelic SNPs on single cells
  ☆150Updated last year
• vanheeringen-lab / seq2science
  Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workf…
  ☆165Updated 4 months ago
• htseq / htseq
  HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.
  ☆106Updated 4 months ago
• 10XGenomics / subset-bam
  ☆81Updated last year
• zktuong / dandelion
  dandelion - A single cell BCR/TCR V(D)J-seq analysis package for 10X Chromium 5' data
  ☆119Updated this week
• wheaton5 / souporcell
  Clustering scRNAseq by genotypes
  ☆189Updated 10 months ago
• theislab / anndata2ri
  Convert between AnnData and SingleCellExperiment
  ☆140Updated last week
• theislab / diffxpy
  Differential expression analysis for single-cell RNA-seq data.
  ☆204Updated 7 months ago
• jackh726 / bigtools
  A high-performance BigWig and BigBed library in Rust
  ☆101Updated 4 months ago
• nf-core / scdownstream
  A single cell transcriptomics pipeline for QC, integration and making the data presentable
  ☆77Updated 3 weeks ago
• timoast / sinto
  Tools for single-cell data processing
  ☆127Updated last year
• haowenz / chromap
  Fast alignment and preprocessing of chromatin profiles
  ☆204Updated 2 weeks ago
• vanheeringen-lab / gimmemotifs
  Suite of motif tools, including a motif prediction pipeline for ChIP-seq experiments. See full GimmeMotifs documentation for detailed in…
  ☆120Updated this week
• singleron-RD / CeleScope
  Single Cell Analysis Pipelines
  ☆107Updated last week
• dohlee / metheor
  Ultrafast DNA methylation heterogeneity calculation from bisulfite alignments (Lee et al., PLOS Computational Biology. 2023)
  ☆47Updated last month
• interactivereport / cellxgene_VIP
  Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey a…
  ☆158Updated last month
• kanaverse / kana
  Single cell analysis in the browser
  ☆151Updated last month
• BUStools / bustools
  Tools for working with BUS files
  ☆101Updated 4 months ago
• scverse / scirpy
  A scanpy extension to analyse single-cell TCR and BCR data.
  ☆239Updated last week
• tavareshugo / tutorial_DESeq2_contrasts
  ☆63Updated last year
• caleblareau / mgatk
  mgatk: mitochondrial genome analysis toolkit
  ☆108Updated 8 months ago
• FredHutch / SEACR
  SEACR: Sparse Enrichment Analysis for CUT&RUN
  ☆112Updated 2 years ago
• kharchenkolab / numbat
  Haplotype-aware CNV analysis from single-cell RNA-seq
  ☆190Updated 2 weeks ago