10x-genomics
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Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
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Mar 11, 2025 - Nextflow
Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
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Apr 20, 2021 - R
List of tools and resources related to the 10x Genomics GEMCode/Chromium system
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Feb 8, 2019
Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.
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Mar 14, 2025 - Nextflow
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
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May 6, 2019 - R
simplified cellranger for long-read data
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Sep 18, 2024 - Python
Standalone tool and library allowing to work with barcoded linked-reads
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Dec 7, 2024 - C++
Collection of tools and resources for linked-reads
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Dec 17, 2024
Sanger Cellular Genetics single-cell ATAC-seq pipeline.
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Aug 25, 2023 - Nextflow
Perform Visium Standard Definition (SD) spot deconvolution into putative single cells using distance-based gene clustering and cell type formulation.
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Mar 11, 2025 - Jupyter Notebook
CWL toolkit for single-cell sequencing data analysis
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Nov 11, 2022 - Common Workflow Language
R package: {rfca} Random forest-based cell annotation methods for scRNAseq analysis. {rfca} contains methods which identifies cell types using machine learning trained on a diversity of cell types, without the need for a labelled training dataset. It also allows you to train your own cell prediction models with your own labels (cell type, subtyp…
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Oct 7, 2020 - R
De novo assembly pipeline for 10X linked-reads using Supernova
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Sep 15, 2020 - Nextflow
R script built on Seurat objects to analyze 10X single-cell expression data
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Dec 14, 2021 - R
Pipeline for SV detection using 10X genomics data
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Oct 8, 2018 - Python
Preliminary study to figure out how many larval gonads are needed for RNA-Seq
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Aug 5, 2020 - Jupyter Notebook
adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data
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Jun 21, 2019 - C++
Scripts developed to work with 10x Genomics sequencing results
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Sep 20, 2017 - R
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