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154

177

mit

130

A single-cell RNAseq pipeline for 10X genomics data

alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics

Created 2019-04-08

1,401 commits to master branch, last one a day ago

iCellR rezakj

19

119

unknown

13

Single (i) Cell R package (iCellR) is an interactive R package to work with high-throughput single cell sequencing technologies (i.e scRNA-seq, scVDJ-seq, scATAC-seq, CITE-Seq and Spatial Transcriptom...

3d umap icellr dropout cite-seq scrna-seq scvdj-seq clustering imputation pseudotime 10xgenomics normalization diffusion-maps intractive-graph batch-normalization clustering-algorithm singel-cell-sequencing cell-type-classification

Created 2018-12-11

83 commits to master branch, last one 3 months ago

arcs bcgsc

16

90

gpl-3.0

25

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

graph genome science scaffold assembler 10xgenomics c-plus-plus pacbio-data bioinformatics oxford-nanopore nanopore-sequencing

Created 2016-06-06

268 commits to master branch, last one 3 months ago

loupeR 10XGenomics

12

80

other

8

Convert Seurat objects to 10x Genomics Loupe files.

r-package 10xgenomics single-cell-genomics

Created 2023-08-23

21 commits to main branch, last one a day ago

spatialLIBD LieberInstitute

16

73

unknown

20

Code for the spatialLIBD R/Bioconductor package and shiny app

golem shiny rstats visium 10xgenomics spatiallibd bioconductor spatialexperiment spatial-transcriptomics

Created 2019-12-04

631 commits to devel branch, last one about a month ago

HumanPilot LieberInstitute

27

64

unknown

18

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

brain dlpfc human rstats visium biorxiv analysis 10xgenomics spatial-transcriptomics

Created 2019-12-04

214 commits to master branch, last one about a month ago

tigmint bcgsc

13

54

gpl-3.0

18

⛓ Correct misassemblies using linked AND long reads

10xgenomics linked-reads bioinformatics genome-assembly genome-scaffolding bioinformatics-tool misassembly-correction

Created 2017-07-22

227 commits to master branch, last one 9 months ago

spatialvi nf-core

13

41

mit

155

Pipeline for processing spatially-resolved gene counts with spatial coordinates and image data. Designed for 10x Genomics Visium transcriptomics.

st visium nf-core rna-seq spatial nextflow pipeline workflow microscopy 10xgenomics single-cell 10x-genomics bioinformatics transcriptomics image-processing spatial-transcriptomics

Created 2022-02-23

611 commits to dev branch, last one about a month ago