R toolkit for single cell genomics
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Aug 27, 2021 - R
#
single-cell-rna-seq
Here are 224 public repositories matching this topic...
Deep probabilistic analysis of single-cell omics data
scrna-seq
variational-autoencoder
variational-bayes
single-cell-genomics
single-cell-rna-seq
deep-generative-model
cite-seq
human-cell-atlas
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Updated
Sep 1, 2021 - Python
c-plus-plus
bioinformatics
rna-seq
gene-expression
rnaseq
scrna-seq
quantification
transcriptome
single-cell
quasi-mapping
salmon
sailfish
10x
single-cell-rna-seq
selective-alignment
rna-seq-quantification
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Updated
Aug 10, 2021 - C++
Table of software for the analysis of single-cell RNA-seq data.
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Updated
Sep 1, 2021 - R
NicheNet: predict active ligand-target links between interacting cells
rna-seq
gene-expression
network-inference
data-integration
single-cell-rna-seq
single-cell-omics
intercellular-communication
ligand-receptor
ligand-target
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Aug 26, 2021 - R
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Updated
Aug 30, 2021 - R
R package for the joint analysis of multiple single-cell RNA-seq datasets
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Updated
Aug 10, 2021 - R
CellRank for directed single-cell fate mapping
data-science
machine-learning
bioinformatics
genetics
trajectory-generation
markov-chains
manifold-learning
single-cell-genomics
single-cell-rna-seq
cell-fate-transitions
fuzzy-clustering-analyses
rna-velocity
cell-fate-determination
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Sep 1, 2021 - Python
R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
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Updated
Aug 12, 2021 - JavaScript
Differential expression analysis for single-cell RNA-seq data.
bioinformatics
tensorflow
transcriptomics
gene-set-enrichment
differential-expression
single-cell-rna-seq
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Jul 15, 2021 - Python
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Aug 17, 2018 - Perl
A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments
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Jun 28, 2021 - R
Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
bioinformatics
statistical-methods
data-visualization
dimensionality-reduction
single-cell-genomics
single-cell-rna-seq
nonnegative-matrix-factorization
single-cell-analysis
single-cell-atac-seq
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Mar 4, 2021 - R
A collection of 50+ trajectory inference methods within a common interface 📥 📤
bioinformatics-algorithms
single-cell-rna-seq
single-cell-analysis
trajectory-inference-methods
trajectory-inference
pseudotemporal-ordering
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Feb 18, 2021 - R
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
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Jul 7, 2021 - R
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
hmm
bioinformatics
bayesian
transcriptomics
subpopulation
heterogeneity
single-cell-rna-seq
single-cell-analysis
cnv-detection
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Jul 19, 2021 - R
A tool for unsupervised projection of single cell RNA-seq data
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Nov 24, 2020 - R
Infer cell types in scRNA-seq data using bulk RNA-seq or gene sets
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Updated
Aug 29, 2021 - R
Single-Cell Clustering Assessment Framework
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Jul 9, 2021 - Jupyter Notebook
integrated RNA-seq Analysis Pipeline
rna-seq
pipeline
gene-expression
rna-seq-analysis
differential-expression
transcript-quantification
single-cell-rna-seq
irap
bulk-rna-seq
exon-quantification
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Feb 6, 2019 - R
Pipeline for initial analysis of droplet-based single-cell RNA-seq data
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Sep 27, 2020 - C++
Accurate and robust imputation of scRNA-seq data
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Aug 21, 2019 - R
Seurat meets tidyverse. The best of both worlds.
ggplot2
dplyr
tidyverse
pca
transcripts
single-cell
tsne
umap
normalization
tibble
tidyr
sct
purrr
single-cell-rna-seq
seurat
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Aug 24, 2021 - R
Cluster single cells and analyze cell clade relationships with colorful visualizations.
visualization
bioinformatics-pipeline
single-cell
bioinformatics-algorithms
single-cell-rna-seq
single-cell-analysis
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Aug 27, 2021 - Haskell
Content for the OSCA Book.
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Aug 29, 2021 - Dockerfile
A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
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Aug 20, 2021 - Python
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
benchmarking
scrna-seq
single-cell
single-cell-rna-seq
single-cell-omics
trajectory-inference-methods
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May 20, 2021 - R
A statistical test for compositional changes in scRNA
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Aug 25, 2021 - Jupyter Notebook
scDeepCluster for Single Cell RNA-seq data
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Jul 16, 2021 - Jupyter Notebook
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Hi,
I find this method really cool and promising but I am having issues trying to implement it to my data.
Can you provide a vignette (or section of one) describing how to go from expression matrix to the necessary input file for MuSiC? Or perhaps you can construct the single cell reference files from the Tabula muris or MCA datasets?