Showing 6 of total 6 results (show query)
csgillespie
benchmarkme:Crowd Sourced System Benchmarks
Benchmark your CPU and compare against other CPUs. Also provides functions for obtaining system specifications, such as RAM, CPU type, and R version.
Maintained by Colin Gillespie. Last updated 11 months ago.
42 stars 9.00 score 118 scripts 14 dependents
bioc
CellBench:Construct Benchmarks for Single Cell Analysis Methods
This package contains infrastructure for benchmarking analysis methods and access to single cell mixture benchmarking data. It provides a framework for organising analysis methods and testing combinations of methods in a pipeline without explicitly laying out each combination. It also provides utilities for sampling and filtering SingleCellExperiment objects, constructing lists of functions with varying parameters, and multithreaded evaluation of analysis methods.
Maintained by Shian Su. Last updated 5 months ago.
softwareinfrastructuresinglecellbenchmarkbioinformatics
31 stars 8.73 score 98 scripts
nanxstats
hdnom:Benchmarking and Visualization Toolkit for Penalized Cox Models
Creates nomogram visualizations for penalized Cox regression models, with the support of reproducible survival model building, validation, calibration, and comparison for high-dimensional data.
Maintained by Nan Xiao. Last updated 7 months ago.
benchmarkhigh-dimensional-datalinear-regressionnomogram-visualizationpenalized-cox-modelssurvival-analysisopenblas
43 stars 8.07 score 68 scripts 1 dependentsbioc
EpiCompare:Comparison, Benchmarking & QC of Epigenomic Datasets
EpiCompare is used to compare and analyse epigenetic datasets for quality control and benchmarking purposes. The package outputs an HTML report consisting of three sections: (1. General metrics) Metrics on peaks (percentage of blacklisted and non-standard peaks, and peak widths) and fragments (duplication rate) of samples, (2. Peak overlap) Percentage and statistical significance of overlapping and non-overlapping peaks. Also includes upset plot and (3. Functional annotation) functional annotation (ChromHMM, ChIPseeker and enrichment analysis) of peaks. Also includes peak enrichment around TSS.
Maintained by Hiranyamaya Dash. Last updated 2 months ago.
epigeneticsgeneticsqualitycontrolchipseqmultiplecomparisonfunctionalgenomicsatacseqdnaseseqbenchmarkbenchmarkingbioconductorbioconductor-packagecomparisonhtmlinteractive-reporting
15 stars 7.49 score 46 scriptsbioc
pipeComp:pipeComp pipeline benchmarking framework
A simple framework to facilitate the comparison of pipelines involving various steps and parameters. The `pipelineDefinition` class represents pipelines as, minimally, a set of functions consecutively executed on the output of the previous one, and optionally accompanied by step-wise evaluation and aggregation functions. Given such an object, a set of alternative parameters/methods, and benchmark datasets, the `runPipeline` function then proceeds through all combinations arguments, avoiding recomputing the same step twice and compiling evaluations on the fly to avoid storing potentially large intermediate data.
Maintained by Pierre-Luc Germain. Last updated 5 months ago.
geneexpressiontranscriptomicsclusteringdatarepresentationbenchmarkbioconductorpipeline-benchmarkingpipelinessingle-cell-rna-seq
41 stars 7.02 score 43 scriptsbioc
benchdamic:Benchmark of differential abundance methods on microbiome data
Starting from a microbiome dataset (16S or WMS with absolute count values) it is possible to perform several analysis to assess the performances of many differential abundance detection methods. A basic and standardized version of the main differential abundance analysis methods is supplied but the user can also add his method to the benchmark. The analyses focus on 4 main aspects: i) the goodness of fit of each method's distributional assumptions on the observed count data, ii) the ability to control the false discovery rate, iii) the within and between method concordances, iv) the truthfulness of the findings if any apriori knowledge is given. Several graphical functions are available for result visualization.
Maintained by Matteo Calgaro. Last updated 4 months ago.
metagenomicsmicrobiomedifferentialexpressionmultiplecomparisonnormalizationpreprocessingsoftwarebenchmarkdifferential-abundance-methods
8 stars 5.78 score 8 scripts