8 results found Sort:

nf-core
scrnaseq nf-core
186
256
mit
140
Single-cell RNA-Seq pipeline for barcode-based protocols such as 10x, DropSeq or SmartSeq, offering a variety of aligners and empty-droplet detection
alevin nf-core rna-seq bustools kallisto nextflow pipeline workflow star-solo cellranger 10xgenomics single-cell 10x-genomics
Created 2019-04-08
1,761 commits to master branch, last one 12 days ago
rezakj
iCellR rezakj
19
122
unknown
12
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
84 commits to master branch, last one 8 months ago
10XGenomics
loupeR 10XGenomics
15
114
other
10
Convert Seurat objects to 10x Genomics Loupe files.
r-package 10xgenomics single-cell-genomics
Created 2023-08-23
35 commits to main branch, last one about a month ago
bcgsc
arcs bcgsc
16
92
gpl-3.0
22
🌈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
272 commits to master branch, last one 4 months ago
LieberInstitute
spatialLIBD LieberInstitute
20
91
unknown
19
Code for the spatialLIBD R/Bioconductor package and shiny app
golem shiny rstats visium 10xgenomics spatiallibd bioconductor spatialexperiment spatial-transcriptomics
Created 2019-12-04
831 commits to devel branch, last one 2 days ago
LieberInstitute
HumanPilot LieberInstitute
31
77
unknown
17
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 10 months ago
nf-core
spatialvi nf-core
20
59
mit
161
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
708 commits to dev branch, last one 9 days ago
bcgsc
tigmint bcgsc
13
58
gpl-3.0
17
⛓ 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 about a year ago