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fastq utilsValidation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.
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babelDeep learning model for single-cell inference of multi-omic profiles from a single input modality.
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scarchesReference mapping for single-cell genomics
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celltypistA tool for semi-automatic cell type annotation
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kmer-homology-paperManuscript for functional prediction of transcriptomic “dark matter” across species
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symphonyEfficient and precise single-cell reference atlas mapping with Symphony
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EDS💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
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scDblFinderMethods for detecting doublets in single-cell sequencing data
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cellSNPPileup biallelic SNPs from single-cell and bulk RNA-seq data
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scarfToolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
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alevin-fry🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
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cellrouterReconstruction of complex single-cell trajectories using CellRouter
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MERINGUEcharacterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
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TangramSpatial alignment of single cell transcriptomic data.
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PandoMultiome GRN inference.
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zellkonverterConversion between scRNA-seq objects
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scGEAToolboxscGEAToolbox: Matlab toolbox for single-cell gene expression analyses
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crop-seqData analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)
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gchromVARCell type specific enrichments using finemapped variants and quantitative epigenetic data
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scCATCHAutomatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
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cellrangerRkitNon-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
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immunarch🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
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netSmoothnetSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
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BEERBEER: Batch EffEct Remover for single-cell data
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dbMAPA 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.
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scHPFSingle-cell Hierarchical Poisson Factorization
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SierraDiscover differential transcript usage from polyA-captured single cell RNA-seq data
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kallistobustoolskallisto | bustools workflow for pre-processing single-cell RNA-seq data
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EWCEExpression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
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SHARPSHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection
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scABCNo description or website provided.
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SpiceMixspatial transcriptome, single cell
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vireoDemultiplexing pooled scRNA-seq data with or without genotype reference
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iDEADifferential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)
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souporcellClustering scRNAseq by genotypes
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mgatkmgatk: mitochondrial genome analysis toolkit
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northstarSingle cell type annotation guided by cell atlases, with freedom to be queer
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vitessceRR API and htmlwidget for Vitessce
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cerebraA tool for fast and accurate summarizing of variant calling format (VCF) files
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HarmonyHarmony framework for connecting scRNA-seq data from discrete time points
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cnaCovarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.
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ALRAImputation method for scRNA-seq based on low-rank approximation
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GCModellerGCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language
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VoxHuntVoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps
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SCopeLoomRR package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
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Awesome Single CellCommunity-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
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cTPnetcTPnet Package
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GLUEGraph-linked unified embedding for single-cell multi-omics data integration
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scPowerExperimental design framework for scRNAseq population studies (eQTL and DE)
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bapBead-based single-cell atac processing
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dropEstPipeline for initial analysis of droplet-based single-cell RNA-seq data
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velodynDynamical systems methods for RNA velocity analysis
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SCOPE-toolsSingle-Cell Omics Preparation Entity Tools
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switchdeInference of switch-like differential expression along single-cell trajectories
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