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Rachel Griffard (rachelgriffard)

rachelgriffard

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Company:University of Kansas Medical Center

Location:Kansas City, KS

Home Page:www.linkedin.com/in/rachelgriffard

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Rachel Griffard's starred repositories

bulk2space

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

Language:Jupyter NotebookLicense:GPL-3.0Stargazers:110Issues:0Issues:0

anndata

Annotated data.

Language:PythonLicense:BSD-3-ClauseStargazers:569Issues:0Issues:0

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language:PythonLicense:BSD-3-ClauseStargazers:1209Issues:0Issues:0

seurat-wrappers

Community-provided extensions to Seurat

Language:RLicense:GPL-3.0Stargazers:298Issues:0Issues:0

SeuratExtend

Language:RLicense:GPL-3.0Stargazers:83Issues:0Issues:0

harmony

Fast, sensitive and accurate integration of single-cell data with Harmony

Language:RLicense:NOASSERTIONStargazers:518Issues:0Issues:0

SpotClean

R package for decontaminating the spot swapping effect and recovering true expression in spatial transcriptomics data

Language:RStargazers:21Issues:0Issues:0

PrinciplesSTA

'Principles of Spatial Transcriptomics Analysis with Bioconductor' book

Language:TeXStargazers:36Issues:0Issues:0

CellChat

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

Language:RLicense:GPL-3.0Stargazers:260Issues:0Issues:0

squidpy

Spatial Single Cell Analysis in Python

Language:PythonLicense:BSD-3-ClauseStargazers:428Issues:0Issues:0

cellrank

CellRank: dynamics from multi-view single-cell data

Language:PythonLicense:BSD-3-ClauseStargazers:342Issues:0Issues:0

SingleCellExperiment

Clone of the Bioconductor repository for the SingleCellExperiment package, see https://bioconductor.org/packages/devel/bioc/html/SingleCellExperiment.html for the official development version.

Language:RStargazers:65Issues:0Issues:0

scvelo

RNA Velocity generalized through dynamical modeling

Language:PythonLicense:BSD-3-ClauseStargazers:411Issues:0Issues:0

seurat

R toolkit for single cell genomics

Language:RLicense:NOASSERTIONStargazers:2258Issues:0Issues:0

go

The Open Source Data Science Masters

License:UnlicenseStargazers:24861Issues:0Issues:0

scCustomize

R package with collection of functions created and/or curated to aid in the visualization and analysis of single-cell data using R.

Language:RLicense:GPL-3.0Stargazers:201Issues:0Issues:0

tidyseurat

Seurat meets tidyverse. The best of both worlds.

Language:RStargazers:155Issues:0Issues:0

voyager

From geospatial to spatial -omics

Language:RLicense:Artistic-2.0Stargazers:70Issues:0Issues:0

scrublet

Detect doublets in single-cell RNA-seq data

Language:Jupyter NotebookLicense:MITStargazers:131Issues:0Issues:0

dittoSeq

Color blindness friendly visualization of single-cell and bulk RNA-sequencing data

Language:RLicense:MITStargazers:186Issues:0Issues:0

splatter

Simple simulation of single-cell RNA sequencing data

Language:RLicense:GPL-3.0Stargazers:214Issues:0Issues:0

TCGAbiolinks

TCGAbiolinks

Language:RStargazers:290Issues:0Issues:0

awesome-omics

A collection of awesome things regarding all omics.

License:MITStargazers:544Issues:0Issues:0

fgsea

Fast Gene Set Enrichment Analysis

Language:RLicense:NOASSERTIONStargazers:369Issues:0Issues:0

Detection_of_cfmDNA

Stargazers:2Issues:0Issues:0

scRNAseq-analysis-notes

scRNAseq analysis notes from Ming Tang

License:MITStargazers:630Issues:0Issues:0

rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Language:NextflowLicense:MITStargazers:873Issues:0Issues:0

Trimmomatic

Language:JavaLicense:NOASSERTIONStargazers:216Issues:0Issues:0

bowtie2

A fast and sensitive gapped read aligner

Language:C++License:GPL-3.0Stargazers:662Issues:0Issues:0

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

Language:JavaScriptLicense:GPL-3.0Stargazers:1205Issues:0Issues:0