Topic: single-cell Goto Github
Some thing interesting about single-cell
Some thing interesting about single-cell
single-cell,pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
Organization: aertslab
Home Page: http://scenic.aertslab.org
single-cell,An overview of algorithms for estimating pseudotime in single-cell RNA-seq data
User: agitter
single-cell,
Organization: bowang-lab
Home Page: https://scgpt.readthedocs.io/en/latest/
single-cell,A software package for analyzing snapshots of developmental processes
Organization: broadinstitute
Home Page: https://broadinstitute.github.io/wot/
single-cell,Deep neural networks for predicting CpG methylation
User: cangermueller
single-cell,Cell type annotation with local Large Language Models (LLMs) - Ensuring privacy and speed with extensive customized reports
Organization: celvoxes
Home Page: https://celvox.co
single-cell,🐟 🔬🦀 alevin-fry is an efficient and flexible tool for processing single-cell sequencing data, currently focused on single-cell transcriptomics and feature barcoding.
Organization: combine-lab
Home Page: https://alevin-fry.readthedocs.io
single-cell,🐟 🍣 🍱 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
single-cell,EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
Organization: digitalcytometry
single-cell,Color blindness friendly visualization of single-cell and bulk RNA-sequencing data
User: dtm2451
single-cell,Generate high quality, publication ready visualizations for single cell transcriptomics data.
User: enblacar
Home Page: https://enblacar.github.io/SCpubr-book/
single-cell,A collection of awesome things regarding all omics.
User: flowhub-team
single-cell,Graph-linked unified embedding for single-cell multi-omics data integration
Organization: gao-lab
single-cell,Papers with code for single cell related papers
User: genecell
single-cell,Collection of public scRNA-Seq datasets used by our group
Organization: hemberg-lab
Home Page: https://hemberg-lab.github.io/scRNA.seq.datasets/
single-cell,R package for analyzing single-cell RNA-seq data
Organization: hms-dbmi
Home Page: http://pklab.med.harvard.edu/scde
single-cell,Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy.
Organization: icbi-lab
Home Page: https://infercnvpy.readthedocs.io/en/latest/
single-cell,🧬 Immunarch: an R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires
Organization: immunomind
Home Page: https://immunarch.com
single-cell,R/shiny interface for interactive visualization of data in SummarizedExperiment objects
Organization: isee
Home Page: https://isee.github.io/iSEE/
single-cell,scGNN (single cell graph neural networks) for single cell clustering and imputation using graph neural networks
User: juexinwang
single-cell,Single cell analysis in the browser
Organization: kanaverse
Home Page: https://kanaverse.org/kana/
single-cell,Haplotype-aware CNV analysis from single-cell RNA-seq
Organization: kharchenkolab
Home Page: https://kharchenkolab.github.io/numbat/
single-cell,R package for analyzing and interactively exploring large-scale single-cell RNA-seq datasets
Organization: kharchenkolab
single-cell,
User: kpatel427
single-cell,PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
Organization: krishnaswamylab
Home Page: http://phate.readthedocs.io
single-cell,Bayesian haplotype-based mutation calling
Organization: luntergroup
single-cell,A list of scRNA-seq analysis tools
User: mdozmorov
single-cell,MiXCR is an ultimate software platform for analysis of Next-Generation Sequencing (NGS) data for immune profiling.
Organization: milaboratory
Home Page: https://mixcr.com
single-cell,A single-cell RNAseq pipeline for 10X genomics data
Organization: nf-core
Home Page: https://nf-co.re/scrnaseq
single-cell,DANCE: a deep learning library and benchmark platform for single-cell analysis
Organization: omicsml
Home Page: https://pydance.readthedocs.io
single-cell,Methods for detecting doublets in single-cell sequencing data
User: plger
Home Page: https://plger.github.io/scDblFinder/
single-cell,Python package to perform enrichment analysis from omics data.
Organization: saezlab
Home Page: https://decoupler-py.readthedocs.io/
single-cell,LIANA+: an all-in-one framework for cell-cell communication
Organization: saezlab
Home Page: http://liana-py.readthedocs.io/
single-cell,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/
single-cell,Table of software for the analysis of single-cell RNA-seq data.
Organization: scrna-tools
Home Page: https://www.scrna-tools.org
single-cell,Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
User: seandavi
single-cell,Efficient genotyping bi-allelic SNPs on single cells
Organization: single-cell-genetics
Home Page: https://cellsnp-lite.readthedocs.io
single-cell,A python library for multi omics included bulk, single cell and spatial RNA-seq analysis.
User: starlitnightly
Home Page: https://starlitnightly.github.io/omicverse/
single-cell,Seurat meets tidyverse. The best of both worlds.
User: stemangiola
Home Page: https://stemangiola.github.io/tidyseurat/
single-cell,R toolkit for the analysis of single-cell chromatin data
Organization: stuart-lab
Home Page: https://stuartlab.org/signac/
single-cell,A tool for semi-automatic cell type classification
Organization: teichlab
Home Page: https://www.celltypist.org/
single-cell,Reference mapping for single-cell genomics
Organization: theislab
Home Page: https://docs.scarches.org/en/latest/
single-cell,Single cell perturbation prediction
Organization: theislab
Home Page: https://scgen.readthedocs.io
single-cell,https://www.sc-best-practices.org
Organization: theislab
Home Page: https://www.sc-best-practices.org
single-cell,RNA velocity estimation in Python
Organization: velocyto-team
Home Page: http://velocyto.org/velocyto.py/
single-cell,Vitessce is a visual integration tool for exploration of spatial single-cell experiments.
Organization: vitessce
Home Page: http://vitessce.io
single-cell,R package for integrating and analyzing multiple single-cell datasets
Organization: welch-lab
single-cell,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/
single-cell,Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data
User: zjufanlab
Home Page: https://www.sciencedirect.com/science/article/pii/S2589004220300663
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