Discover lmweber/benchmarking-guidelines Open Source project

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R
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MIT License
Created over 6 years ago
Updated almost 6 years ago

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Drafts of our review paper "Essential Practical Guidelines for Benchmarking Computational Methods"

cytometry-clustering-comparison

R scripts to reproduce analyses in our paper comparing clustering methods for high-dimensional cytometry data

BestPracticesST

'Best Practices for Spatial Transcriptomics Analysis with Bioconductor' online book

TeX

diffcyt

R package for differential discovery analyses in high-dimensional cytometry data

deconvolution-papers

List of papers on deconvolution of cell types in bulk RNA-seq based on single-cell signatures

Rtsne-example

Short example showing how to calculate and plot a 2D t-SNE projection from mass cytometry data in R

FlowSOM-Rtsne-example

Worked example showing how to cluster and visualize flow/mass cytometry data using FlowSOM and Rtsne

nnSVG

nnSVG: scalable method to identify spatially variable genes (SVGs) in spatially-resolved transcriptomics data

HDCytoData

Data package containing high-dimensional cytometry data sets in SummarizedExperiment and flowSet formats

benchmark-data-Levine-32-dim

R code to prepare 32-dimensional CyTOF benchmark data set from Levine et al. (2015), for testing high-dimensional clustering algorithms

diffcyt-evaluations

Scripts to reproduce evaluations and figures in our paper introducing the 'diffcyt' framework

PD1_analysis_CellCnn

Code to run CellCnn analyses in collaboration paper by Krieg et al. (2018), Nature Medicine

snp-dmx-cancer

Reproducible code for workflow and evaluations in our paper evaluating genetic variation-based demultiplexing tools in cancer

Shell

locus-c

Code to reproduce analyses in our paper on the landscape of gene expression in the human locus coeruleus (LC)

HTML

regsplice

R package for detection of differential exon usage in RNA-seq and exon microarray data

cytometry-trees

Cytometry clustering trees

CyTOF-workshop-2017-07-10

Information and teaching materials for CyTOF workshop (R sessions), University of Zurich, 10-12 July 2017

HDCytoData-example

R code to reproduce example in Figure 1 in our HDCytoData paper

glmnet-error-example

Reproducible example to demonstrate possible bug in glmnet version 2.0-2

clustermatch

R package for matching detected clusters to true clusters and evaluating performance

benchmark-data-Levine-13-dim

R code to prepare 13-dimensional CyTOF benchmark data set from Levine et al. (2015), for testing high-dimensional clustering algorithms

WeberDivechaLCdata

Data package containing single-nucleus and spatially-resolved gene expression data from the human locus coeruleus (LC)

nnSVG-analyses

Scripts to reproduce analyses and figures in nnSVG paper

useful-commands

Collection of useful commands and keyboard shortcuts for Mac and Linux

cytometry-perplexed

R scripts to generate figures in our paper Liechti et al. (2021)

STexampleData

Collection of spatially resolved transcriptomics datasets in SpatialExperiment R/Bioconductor format

ggspavis

Visualization functions for spatially resolved transcriptomics data

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