Topic: scrna-seq Goto Github
Some thing interesting about scrna-seq
Some thing interesting about scrna-seq
scrna-seq,R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.
User: antoniodefalco
Home Page: https://www.nature.com/articles/s41467-023-36790-9
scrna-seq,Inclusive model of expression dynamics with conventional or metabolic labeling based scRNA-seq / multiomics, vector field reconstruction and differential geometry analyses
Organization: aristoteleo
Home Page: https://dynamo-release.readthedocs.io/en/latest/
scrna-seq,Spatial alignment of single cell transcriptomic data.
Organization: broadinstitute
scrna-seq,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
User: catavallejos
scrna-seq,single cell Flux Estimation Analysis (scFEA) Try the below web server!
User: changwn
Home Page: http://scflux.org/
scrna-seq,An interactive explorer for single-cell transcriptomics data
Organization: chanzuckerberg
Home Page: https://chanzuckerberg.github.io/cellxgene/
scrna-seq,🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
Organization: combine-lab
Home Page: https://combine-lab.github.io/salmon
scrna-seq,A tool for fast and accurate summarizing of variant calling format (VCF) files
Organization: czbiohub-sf
scrna-seq,a fully Bayesian approach to deconvolve tumor microenvironment
Organization: danko-lab
scrna-seq,Single cell trajectory detection
Organization: dpeerlab
Home Page: https://palantir.readthedocs.io
scrna-seq,A set of tools supporting the development, execution, and benchmarking of trajectory inference methods. 🌍
Organization: dynverse
Home Page: http://dynverse.org
scrna-seq,Deep Embedding for Single-cell Clustering
User: eleozzr
Home Page: https://eleozzr.github.io/desc/
scrna-seq,Papers with code for single cell related papers
User: genecell
scrna-seq,Fast, sensitive and accurate integration of single-cell data with Harmony
Organization: immunogenomics
Home Page: https://portals.broadinstitute.org/harmony/
scrna-seq,Efficient and precise single-cell reference atlas mapping with Symphony
Organization: immunogenomics
scrna-seq,Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
User: interactivereport
Home Page: https://cellxgenevip-ms.bxgenomics.com
scrna-seq,Doublet detection in single-cell RNA-seq data.
User: jonathanshor
Home Page: https://doubletdetection.readthedocs.io/en/stable/
scrna-seq,Useful functions to make your scRNA-seq plot more cool!
User: junjunlab
scrna-seq,R package for the joint analysis of multiple single-cell RNA-seq datasets
Organization: kharchenkolab
scrna-seq,Pipeline for initial analysis of droplet-based single-cell RNA-seq data
Organization: kharchenkolab
scrna-seq,R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Organization: kharchenkolab
scrna-seq,Imputation method for scRNA-seq based on low-rank approximation
Organization: klugerlab
scrna-seq,Bring your single-cell data to life
Organization: lilab-bcb
Home Page: https://cirrocumulus.readthedocs.io/
scrna-seq,Single-cell Transcriptome and Regulome Analysis Pipeline
User: liulab-dfci
scrna-seq,A list of scRNA-seq analysis tools
User: mdozmorov
scrna-seq,Simple simulation of single-cell RNA sequencing data
Organization: oshlack
scrna-seq,A wrapper for the kallisto | bustools workflow for single-cell RNA-seq pre-processing
Organization: pachterlab
Home Page: https://www.kallistobus.tools/
scrna-seq,Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.
User: parashardhapola
Home Page: http://scarf.readthedocs.io
scrna-seq,Assessing the purity of single cell population
User: paulingliu
scrna-seq,STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data
Organization: pinellolab
Home Page: http://stream.pinellolab.org
scrna-seq,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 Transcriptomics (ST)).
User: rezakj
scrna-seq,MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data
Organization: saeyslab
scrna-seq,R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.
User: samuel-marsh
Home Page: https://samuel-marsh.github.io/scCustomize/
scrna-seq,scPerturb: A resource and a python/R tool for single-cell perturbation data
Organization: sanderlab
Home Page: http://www.sanderlab.org/scPerturb/
scrna-seq,Table of software for the analysis of single-cell RNA-seq data.
Organization: scrna-tools
Home Page: https://www.scrna-tools.org
scrna-seq,muon is a multimodal omics Python framework
Organization: scverse
Home Page: https://muon.scverse.org/
scrna-seq,Deep probabilistic analysis of single-cell and spatial omics data
Organization: scverse
Home Page: http://scvi-tools.org/
scrna-seq,Single-cell Hierarchical Poisson Factorization
Organization: simslab
scrna-seq,Demultiplexing pooled scRNA-seq data with or without genotype reference
Organization: single-cell-genetics
Home Page: https://vireoSNP.readthedocs.io
scrna-seq,A tool for semi-automatic cell type harmonization and integration
Organization: teichlab
scrna-seq,A tool for semi-automatic cell type classification
Organization: teichlab
Home Page: https://www.celltypist.org/
scrna-seq,The Compositional Perturbation Autoencoder (CPA) is a deep generative framework to learn effects of perturbations at the single-cell level. CPA performs OOD predictions of unseen combinations of drugs, learns interpretable embeddings, estimates dose-response curves, and provides uncertainty estimates.
Organization: theislab
scrna-seq,Reference mapping for single-cell genomics
Organization: theislab
Home Page: https://docs.scarches.org/en/latest/
scrna-seq,Single cell perturbation prediction
Organization: theislab
Home Page: https://scgen.readthedocs.io
scrna-seq,Conversion between scRNA-seq objects
Organization: theislab
Home Page: https://theislab.github.io/zellkonverter/
scrna-seq,Cell2Sentence turns scRNA-seq data into text for LLM training.
Organization: vandijklab
scrna-seq,Clustering scRNAseq by genotypes
User: wheaton5
scrna-seq,An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
User: zhanghao-njmu
Home Page: https://zhanghao-njmu.github.io/SCP/
scrna-seq,a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles
User: zjufanlab
scrna-seq,Cell-type Annotation for Single-cell Transcriptomics using Deep Learning with a Weighted Graph Neural Network
User: zjufanlab
Home Page: https://doi.org/10.1093/nar/gkab775
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