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Search results for single cell
single-cell
x
325 search results found
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
Velodyn
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15
Dynamical systems methods for RNA velocity analysis
Eds
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15
💡 💾 💽 A simple, intuitive and Efficient single cell binary Data Storage format
Omicssuite.github.io
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15
OmicsSuite website for releasing new version.
Deconvolution2016
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15
Code and manuscript files for Aaron and Karsten's deconvolution paper.
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
Hadge
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14
Comprehensive pipeline for donor demultiplexing in single cell
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
Schlapers
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14
Code to run the scHLApers pipeline for personalized single-cell HLA quantification
Uncurl_python
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14
UNCURL is a tool for single cell RNA-seq data analysis.
Cellrangerrkit
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14
Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)
Maegatk
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14
Mitochondrial Alteration Enrichment and Genome Analysis Toolkit
Bgeedb_r
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13
Source code of the R packge BgeeDB to use data from the Bgee database
Singlecellworkflow
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13
Tutorial for the analysis of scRNA-seq data in R
Chromscape
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13
ChromSCape
Lr Splitpipe
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13
Demultiplexing and debarcoding tool designed for LR-Split-seq data.
Mdmcleaner
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13
MDMcleaner the assessment, classification and refinement tool for microbial dark matter SAGs and MAGs
Clustassess
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13
Tools for assessing clustering robustness
Scope Tools
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13
Single-Cell Omics Preparation Entity Tools
Pysinglecellnet
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12
singleCellNet in Python
Gctree
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12
GCtree: phylogenetic inference of genotype-collapsed trees
Fastintegration
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12
FastIntegrate integrates thousands of scRNA-seq datasets and outputs batch-corrected values for downstream analysis
Scaanet
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12
Single-cell archetypal analysis neural network
Scasa
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12
SCASA: Single cell transcript quantification tool
Rna Combine
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11
RNA-seq data comprehensive data analysis toolbox
Gsfa
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11
R package that performs sparse factor analysis and differential gene expression discovery simultaneously on single-cell CRISPR screening data.
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.
Couplednmf
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11
Coupled clustering of single cell genomic data
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
Topicvelo
⭐
11
TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems
Dendro
⭐
11
Genetic Heterogeneity Profiling by Single Cell RNA Sequencing
Scorect
⭐
11
Automated Cell Type Annotation
Vite
⭐
10
R package for analysis of single-cell data using graphs
Gear
⭐
10
The gEAR Portal was created as a data archive and viewer for gene expression data including microarrays, bulk RNA-Seq, single-cell RNA-Seq and more.
Scbs
⭐
10
Python package with CLI for downstream analysis of single cell methylation data.
Scbean
⭐
10
Single-cell data analysis
Humanliver
⭐
10
R Data: Single cell RNA sequencing of human liver reveals distinct intrahepatic macrophage populations
Scmeta
⭐
10
A python library for single-cell metabolism data analysis.
Ursm
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10
A Unified RNA Sequencing Model (URSM) for joint analysis of single cell and bulk RNA-seq data.
Apackoftheclones
⭐
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.
Tidytof
⭐
10
An R package for analyzing high-dimensional cytometry data using the tidyverse.
Nasqar
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10
NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization
Transmorph
⭐
10
Computational framework for dataset integration
Proatac
⭐
10
Preprocessing pipeline for (sc)ATAC data
Iscandar
⭐
10
Interactive reporting tool for single cell RNA-seq data.
Trisicell
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9
Scalable tumor phylogeny inference and validation from single-cell RNA or DNA data
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
Hummus
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9
Molecular interactions inference from single-cell multi-omics data
Grappolo
⭐
9
R package to cluster single-cell data and generate features that can be used for model building
Singlecell Qtl
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9
Discovery and characterization of variance QTLs in human induced pluripotent stem cells
Marcopolo
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9
MarcoPolo is a clustering-free approach to the exploration of bimodally expressed genes along with group information in single-cell RNA-seq data
Singlecellhaystack Py
⭐
8
Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
Irescue
⭐
8
A tool to quantify transposable elements expression in scRNA-seq
Scatac Mouse Human Control
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8
Mouse / human control of cross-contaminations in single-cell ATAC-seq on Fluidigm C1
Mtd
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8
MTD: a unique pipeline for host and meta-transcriptome joint and integrative analyses of RNA-seq data
Ngs17
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8
Materials used during #NGSchool2017
Cemba_data
⭐
8
Mapping pipeline for snmC-seq based technologies.
Vega
⭐
8
VEGA: VAE Enhanced by Gene Annotations
Iasva
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8
Iteratively Adjusted Surrogate Variable Analysis
Immuneaging2017
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8
Code for Celia and Nils' immune aging project.
Fatecompass
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8
Cellcano
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8
Supervised cell type identification for scATAC-seq data
Scgv
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8
SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer
Scarlet
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7
SCARLET (Single-cell Algorithm for Reconstructing Loss-supported Evolution of Tumors) is an algorithm that reconstructs tumor phylogenies from single-cell DNA sequencing data. SCARLET uses a loss-supported model that constrains mutation losses based on observed copy-number data.
Rcellmarker
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7
Identify cell type based on cell markers for single cell squencing
Mudcod
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7
MuDCoD: Multi-subject Dynamic Community Detection
Seuratwizard
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7
This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.
Epigenomics_cwl
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7
SCREW: A Reproducible Workflow for Single-Cell Epigenomics
Discotoolkit_py
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7
DISCO by Scientist for Scientist for You
Single Cell Experiments
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7
Experiments to run single cell analyses efficiently at scale using Zarr, anndata, Scanpy, and Apache Spark
Tirp
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7
code repository for Lagattuta et al. "Repertoire analyses reveal T cell receptor sequence features that influence T cell fate." Nat. Imm. (2022)
Clustifyrdatahub
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7
External single-cell mRNA sequencing data sets for use with clustifyr
Scmmd
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7
Maximum mean discrepancy comparisons for single cell profiling experiments
Plexdia
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7
Multiplexed data-independent acquisition (plexDIA) for increasing proteomics throughput. The code is distributed by an MIT license.
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
Histojs
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7
HistoJS: Web-Based Analytical Tool for Multiplexed Images. Limited Github Online Demo 👇
Archr H5ad
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7
Parse ArchR arrow files to anndata h5ad
Resvae
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7
resVAE is a restricted latent variational autoencoder that we wrote to uncover hidden structures in gene expression data, especially using single-cell RNA sequencing. In principle it can be used with any hierarchically structured data though, so feel free to play around with it.
Disc
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7
A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.
Ananseseurat
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6
Single cell ANANSE Gene-regulatory-network analysis from Seurat objects
Plateeffects2016
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6
Code and manuscript files for Aaron's plate effect paper.
Fast Higashi
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6
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, tensor decomposition
Pixelator
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6
A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.
Neuroblastoma
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6
Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis
Fucci Seq
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6
Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
Signals
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6
Single Cell Genomes with Allele Specificity
Vitessce Data
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6
Utils for loading HuBMAP data formats
Dea_seurat
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6
A Snakemake workflow for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.
Scghost
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6
single-cell Hi-C, scHi-C, Hi-C, 3D genome, nuclear organization, genome subcompartment
Scruff
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6
Single Cell RNA-seq UMI Filtering Facilitator
Pyscnet
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6
A python package for single cell network analysis
Scplant
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6
A versatile framework for single-cell transcriptomic data analysis in plants.
Dturtle
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6
Perform differential transcript usage (DTU) analysis of bulk or single-cell RNA-seq data. See documentation at:
Scmagic
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6
Accurately annotating scRNA-seq data using two rounds of reference-based classification
Nvtk
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6
NvTK (NvwaToolKit), is a systemmatic and easy-using deep learning software in single-cell genomics.
Sclane
⭐
6
Characterize gene dynamics over trajectories using GLMs, GEEs, & GLMMs.
Related Searches
R Single Cell (121)
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