single-cell-genetics

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10 repositories

XClone
Public
Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
cancer-genomics cnv single-cell-rna-seq single-cell-analysis cnv-detection spatial-transcriptomics cna-detection
Python
•
Apache License 2.0
•3•36•9•0•Updated Oct 11, 2024Oct 11, 2024
MQuad
Public
Tool for modelling of mitochondrial heteroplasmy
single-cell-sequencing mitochondria-variant lineage-reconstruction
Python
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Apache License 2.0
•8•16•1•0•Updated Jul 16, 2024Jul 16, 2024
singlecell_neuroseq_paper
Public template
Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation
eqtl ipsc scrna-seq
Jupyter Notebook
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Apache License 2.0
•6•21•1•0•Updated Jun 28, 2024Jun 28, 2024
optimising_singlecell_eqtl_paper
Public
Repository containing the code to reproduce the analyses contained in our manuscript: Optimising expression quantitative trait locus mapping workflows for single-cell studies
single-cell sc-eqtl
Jupyter Notebook
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Apache License 2.0
•1•5•0•0•Updated Jun 28, 2024Jun 28, 2024
singlecell_endodiff_paper
Public
Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression
scrna-seq eqtl ipsc-differentiation
Jupyter Notebook
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Apache License 2.0
•6•15•2•0•Updated Jun 28, 2024Jun 28, 2024
limix_qtl
Public
Python
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Apache License 2.0
•14•20•4•1•Updated Jun 26, 2024Jun 26, 2024
cellsnp-lite
Public
Efficient genotyping bi-allelic SNPs on single cells
single-cell genetic-variants genotyping
C
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Apache License 2.0
•11•142•41•0•Updated Jun 18, 2024Jun 18, 2024
vireo
Public
Demultiplexing pooled scRNA-seq data with or without genotype reference
scrna-seq variational-inference demultiplex single-cells donor-deconvolution
Python
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Apache License 2.0
•27•81•49•1•Updated May 23, 2024May 23, 2024
cardelino
Public
Clone identification from single-cell data
scrna-seq somatic-mutations gibbs-sampling clonal-clustering single-cell
R
•13•61•1•0•Updated Nov 10, 2022Nov 10, 2022
cellSNP
Public
Pileup biallelic SNPs from single-cell and bulk RNA-seq data
rna-seq single-cell genetic-variants genotyping
Python
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Apache License 2.0
•11•77•11•0•Updated Jun 9, 2022Jun 9, 2022