Topic: single-cell-genomics Goto Github
Some thing interesting about single-cell-genomics
Some thing interesting about single-cell-genomics
single-cell-genomics,Convert Seurat objects to 10x Genomics Loupe files.
Organization: 10xgenomics
Home Page: https://10xgen.com/louper
single-cell-genomics,Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.
User: asmagen
Home Page: http://dx.doi.org/10.1016/j.celrep.2019.10.131
single-cell-genomics,Tutorials, workflows, and convenience scripts for Single Cell Portal
Organization: broadinstitute
Home Page: https://singlecell.broadinstitute.org/single_cell
single-cell-genomics,Rails/Docker application for the Broad Institute's single cell RNA-seq data portal
Organization: broadinstitute
Home Page: https://singlecell.broadinstitute.org
single-cell-genomics,Semi-supervised adversarial neural networks for classification of single cell transcriptomics data
Organization: calico
Home Page: https://scnym.research.calicolabs.com
single-cell-genomics,R package for ReDeeM: single-cell Regulatory multi-omics with Deep Mitochondrial mutation profiling.
User: chenweng1991
Home Page: https://chenweng1991.github.io/redeemR/
single-cell-genomics,Finding surprising needles (=features) in haystacks (=single cell/spatial genomics data).
User: ddiez
Home Page: https://ddiez.github.io/singleCellHaystack-py/
single-cell-genomics,Single cell trajectory detection
Organization: dpeerlab
Home Page: https://palantir.readthedocs.io
single-cell-genomics,Generate high quality, publication ready visualizations for single cell transcriptomics data.
User: enblacar
Home Page: https://enblacar.github.io/SCpubr-book/
single-cell-genomics,Evaluation framework for computationally inferred gene networks from single-cell data.
Organization: engreitzlab
single-cell-genomics,Predict RNA velocity through deep learning
Organization: guangyuwanglab2021
Home Page: https://guangyuwanglab2021.github.io/cellDancer_website/
single-cell-genomics,Codes for paper: AWGAN: A Powerful Batch Effect Removal Model for scRNA-seq Data
User: helloworldlty
single-cell-genomics,:ear_of_rice: Zhang, et al, Nature Immunology, 2019. Use single-cell transcriptomics and proteomics to study autoimmune diseases.
Organization: immunogenomics
Home Page: https://www.niams.nih.gov/grants-funding/funded-research/accelerating-medicines
single-cell-genomics,a web application to annotate and visualise single-cell sequencing data using neural networks
Organization: jst-seminar-rostlab-tum
Home Page: https://www.genecruncher.com/#/
single-cell-genomics,Online single-cell data integration through projecting heterogeneous datasets into a common cell-embedding space
User: jsxlei
single-cell-genomics,Single-cell epigenomics analysis tools
User: kaizhang
Home Page: https://kzhang.org/SnapATAC2/
single-cell-genomics,SCGV is an interactive graphical tool for single-cell genomics data, with emphasis on single-cell genomics of cancer
Organization: krasnitzlab
single-cell-genomics,Calibrated clustering via knockoffs for single-cell genomics
Organization: lcrawlab
Home Page: https://lcrawlab.github.io/callback/
single-cell-genomics,A deep learning architecture for robust inference and accurate prediction of cellular dynamics
User: liqian-xc
Home Page: https://sctour.readthedocs.io
single-cell-genomics,Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data
Organization: microsoft
Home Page: https://microsoft.github.io/Nclusion.jl/
single-cell-genomics,An R-based interface for loom files
User: mojaveazure
single-cell-genomics,Interfaces for HDF5-based Single Cell File Formats
User: mojaveazure
Home Page: https://mojaveazure.github.io/seurat-disk
single-cell-genomics,A web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat v3
User: nasqar
Home Page: http://nasqar.abudhabi.nyu.edu/SeuratV3Wizard
single-cell-genomics,This is a web-based interactive (wizard style) application to perform a guided single-cell RNA-seq data analysis and clustering based on Seurat.
User: nasqar
Home Page: http://nasqar.abudhabi.nyu.edu
single-cell-genomics,Visualize cancer genomes with FAIR single-cell RNA-seq data
Organization: ncbi-hackathons
Home Page: https://broad.io/single-cell-bioit-2019
single-cell-genomics,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
single-cell-genomics,Code to reproduce analysis and figures for 'Genetic mapping of etiologic brain cell types for obesity' (Timshel, eLife 2020)
Organization: perslab
Home Page: https://elifesciences.org/articles/55851
single-cell-genomics,𝒫robabilistic modeling of RNA velocity ⬱
Organization: pinellolab
Home Page: https://docs.pyrovelocity.net
single-cell-genomics,Analysis of Single Cell Expression, Normalization and Differential expression
Organization: powellgenomicslab
single-cell-genomics,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.
User: qile0317
Home Page: https://qile0317.github.io/APackOfTheClones/
single-cell-genomics,A deep learning-based tool for alignment and integration of single cell genomic data across multiple datasets, species, conditions, batches
Organization: quon-titative-biology
single-cell-genomics,<<------ Use SnapATAC!!
User: r3fang
single-cell-genomics,Cloud-based single-cell copy-number variation analysis tool
User: robertaboukhalil
Home Page: qb.cshl.edu/ginkgo
single-cell-genomics,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-genomics,A Shiny web app for mapping datasets using Seurat v4
Organization: satijalab
Home Page: https://satijalab.org/azimuth
single-cell-genomics,R toolkit for single cell genomics
Organization: satijalab
Home Page: http://www.satijalab.org/seurat
single-cell-genomics,Dataset distribution for Seurat
Organization: satijalab
single-cell-genomics,Docker images of Seurat
Organization: satijalab
Home Page: https://hub.docker.com/r/satijalab/seurat
single-cell-genomics,Community-provided extensions to Seurat
Organization: satijalab
single-cell-genomics,Deep probabilistic analysis of single-cell and spatial omics data
Organization: scverse
Home Page: http://scvi-tools.org/
single-cell-genomics,Spatial Single Cell Analysis in Python
Organization: scverse
Home Page: https://squidpy.readthedocs.io/en/stable/
single-cell-genomics,CellRank: dynamics from multi-view single-cell data
Organization: theislab
Home Page: https://cellrank.org
single-cell-genomics,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
single-cell-genomics,Reference mapping for single-cell genomics
Organization: theislab
Home Page: https://docs.scarches.org/en/latest/
single-cell-genomics,Single cell perturbation prediction
Organization: theislab
Home Page: https://scgen.readthedocs.io
single-cell-genomics,Various utility functions for Seurat single-cell analysis
User: vertesy
Home Page: https://vertesy.github.io/Seurat.utils
single-cell-genomics,Big data Regression for predicting DNase I hypersensitivity
User: weiqiangzhou
single-cell-genomics,Similarity Weighted Nonnegative Embedding (SWNE), a method for visualizing high dimensional datasets
User: yanwu2014
single-cell-genomics,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/
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