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single-cell
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122 search results found
Scrna Seq_notes
⭐
478
A list of scRNA-seq analysis tools
Liger
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360
R package for integrating and analyzing multiple single-cell datasets
Immunarch
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256
🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Scp
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253
An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
Zumis
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232
zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs
Youtubetutorials
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180
Sccatch
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171
Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
Scde
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163
R package for analyzing single-cell RNA-seq data
Dittoseq
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153
Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
Sccustomize
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142
R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
Tidyseurat
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131
Seurat meets tidyverse. The best of both worlds.
Numbat
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122
Haplotype-aware CNV analysis from single-cell RNA-seq
Scrna.seq.datasets
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121
Collection of public scRNA-Seq datasets used by our group
Scdblfinder
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118
Methods for detecting doublets in single-cell sequencing data
Ecotyper
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118
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
Scpubr
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117
Generate high quality, publication ready visualizations for single cell transcriptomics data.
Powsimr
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102
Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.
Seurat Data
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101
Dataset distribution for Seurat
Scatac Benchmarking
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92
Benchmarking computational single cell ATAC-seq methods
Mgatk
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89
mgatk: mitochondrial genome analysis toolkit
Pando
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88
Multiome GRN inference.
Basics
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81
BASiCS: Bayesian Analysis of Single-Cell Sequencing Data. This is an unstable experimental version. Please see http://bioconductor.org/packages/BASiCS/ for the official release version
Scgate
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79
marker-based purification of cell types from single-cell RNA-seq datasets
Curatedatlasqueryr
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70
Tidy R query API for the harmonised and curated CELLxGENE single-cell atlas.
Singlecellhaystack
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68
Finding surprising needles (=genes) in haystacks (=single cell transcriptome data).
Scatac Pro
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64
A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data
Single Cell Training
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63
SIB course on single cell transcriptomics by mostly using the Seurat pipeline
Scavenge
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60
SCAVENGE is a method to optimize the inference of functional and genetic associations to specific cells at single-cell resolution.
Dynverse
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58
A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
Scperturb
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56
scPerturb: A resource and a python/R tool for single-cell perturbation data
Scmerge
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53
Statistical approach for removing unwanted variation from multiple single-cell datasets
Dyngen
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52
Simulating single-cell data using gene regulatory networks 📠
Scflow
⭐
50
Single-cell/nuclei RNA-seq analysis tools in R for a complete workflow.
Nebulosa
⭐
50
R package to visualize gene expression data based on weighted kernel density estimation
Magma_celltyping
⭐
50
Find causal cell-types underlying complex trait genetics
Ewce
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46
Expression Weighted Celltype Enrichment. See the package website for up-to-date instructions on usage.
Scclustviz
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42
Explore and share your scRNAseq clustering results
Celltalker
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41
Inference of cell-cell communication from single-cell RNAseq data
Sccomp
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37
Robust differential composition and variability analysis for single-cell data
Spatalk
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37
Knowledge-graph-based cell-cell communication inference for spatially resolved transcriptomic data
Scpower
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36
Experimental design framework for scRNAseq population studies (eQTL and DE)
Scpa
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33
R package for pathway analysis in scRNA-seq data
Meringue
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33
characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities
Scmca
⭐
32
Mouse cell atlas
Sscclust
⭐
32
simpler single cell RNAseq data clustering
Cytomapper
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31
R package for visualization of highly multiplexed imaging data
Cytometry Clustering Comparison
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30
R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data
Ouija
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29
Descriptive probabilistic marker gene approach to single-cell pseudotime inference
Scalign
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28
A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
Scmega
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28
scMEGA: Single-cell Multiomic Enhancer-based Gene regulAtory network inference
Csbb Shiny
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28
Computational Suite for Bioinformaticians and Biologists (CSBB) is a RShiny application developed with an intention to empower researchers from wet and dry lab to perform downstream Bioinformatics analysis
Seuratv3wizard
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26
A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
Clonealign
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25
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
M3drop
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24
Tweedieverse
⭐
24
Differential analysis of multi-omics data based on the Tweedie distribution
Bitfam
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23
BITFAM is a Bayesian approach and platform to infer transcription factor activities within individual cells using single cell RNA-sequencing data. Please see Gao S et al., Genome Research (2021) https://genome.cshlp.org/content/31/7/1296 for details.
Beyondcell
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23
Beyondcell is a computational methodology for identifying tumour cell subpopulations with distinct drug responses in single-cell RNA-seq data and proposing cancer-specific treatments.
Scopeloomr
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23
R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...
Citefuse
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23
CiteFuse:
Popsicler
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22
popsicleR, a flexible R package aimed at providing most of the necessary quality controls and preliminary information for complete and detailed analysis of single cell RNA-seq data.
Spark
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22
Spatially resolved transcriptomic analysis
Seurat.utils
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19
Various utility functions for Seurat single-cell analysis
Gchromvar
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18
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Medusa
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18
MeDuSA is a fine-resolution cellular deconvolution method that leverages scRNA-seq data as a reference to estimate cell-state abundance in bulk RNA-seq data.
Scp
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18
Single cell proteomics data processing
Frmatch
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18
Cell type matching in single-cell RNA-sequencing data using FR-Match
Netsmooth
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18
netSmooth: A Network smoothing based method for Single Cell RNA-seq imputation
Imcrtools
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18
An R package for handling and analysing imaging mass cytometry data
Tidygate
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18
Label elements within user drawn gates
Muto_wilson_ncomm_2020
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17
Workflow for analysis of healthy human kidney by snRNAseq and snATACseq
Scmiko
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17
R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.
Elefhant
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17
Ensemble Learning for Harmonization and Annotation of Single Cells (ELeFHAnt) provides an easy to use R package for users to annotate clusters of single cells, harmonize labels across single cell datasets to generate a unified atlas and infer relationship among celltypes between two datasets. It uses an ensemble of three machine learning classifiers 1) RF 2) SVM and 3) LR
Switchde
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15
Inference of switch-like differential expression along single-cell trajectories
Dropclust
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15
Version 2.1.0 released
Sclink
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15
Inferring gene co-expression networks from single cell gene expression data
Splatter Paper
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15
Data and analysis for the Splatter paper
Sctenifoldnet
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14
A R/MATLAB package to construct and compare gene regulatory networks from single-cell transcriptomic data
Scmet
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14
Bayesian modelling of DNA methylation heterogeneity at single-cell resolution
Cellrangerrkit
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14
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
Clustassess
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13
Tools for assessing clustering robustness
Chromscape
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13
ChromSCape
Singlecellworkflow
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13
Tutorial for the analysis of scRNA-seq data in R
Bgeedb_r
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13
Source code of the R packge BgeeDB to use data from the Bgee database
Fastintegration
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12
FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
Scasa
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12
SCASA: Single cell transcript quantification tool
Adtnorm
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11
ADTnorm normalizes the cell surface protein measurement of CITE-seq data, facilitating across batches and across studies data integration.
Clustermole
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11
Unbiased single-cell transcriptomic data cell type identification
Borges
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11
Antique or modern atlas-like depictions of non-linear dimensionality reduction for single cell data
Dendro
⭐
11
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Tidytof
⭐
10
An R package for analyzing high-dimensional cytometry data using the tidyverse.
Apackoftheclones
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10
Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.
Humanliver
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10
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Grappolo
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9
R package to cluster single-cell data and generate features that can be used for model building
Scrank
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9
A computational method to rank and infer drug-responsive cell population towards in-silico drug perturbation using a target-perturbed gene regulatory network (tpGRN) for single-cell transcriptomic data
Immuneaging2017
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8
Code for Celia and Nils' immune aging project.
Iasva
⭐
8
Iteratively Adjusted Surrogate Variable Analysis
Mtd
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8
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Rcellmarker
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7
Identify cell type based on cell markers for single cell squencing
Clustifyrdatahub
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7
External single-cell mRNA sequencing data sets for use with clustifyr
Trendcatcher
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7
TrendCatcher is an open source R-package that allows users to systematically analyze and visualize time course data. Please cite "Temporal transcriptomic analysis using TrendCatcher identifies early and persistent neutrophil activation in severe COVID-19" by Xinge Wang et al published in JCI Insight (2022) - https://insight.jci.org/articles/view/157255
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