IOBR - Immune Oncology Biological Research
Provides six modules for tumor microenvironment (TME) analysis based on multi-omics data. These modules cover data preprocessing, TME estimation, TME infiltrating patterns, cellular interactions, genome and TME interaction, and visualization for TME relevant features, as well as modelling based on key features. It integrates multiple microenvironmental analysis algorithms and signature estimation methods, simplifying the analysis and downstream visualization of the TME. In addition to providing a quick and easy way to construct gene signatures from single-cell RNA-seq data, it also provides a way to construct a reference matrix for TME deconvolution from single-cell RNA-seq data. The analysis pipeline and feature visualization are user-friendly and provide a comprehensive description of the complex TME, offering insights into tumour-immune interactions (Zeng D, et al. (2024) <doi:10.1016/j.crmeth.2024.100910>. Fang Y, et al. (2025) <doi:10.1002/mdr2.70001>).
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geneexpressiondifferentialexpressionimmunooncologytranscriptomicsclusteringsurvivalvisualizationimmuno-oncologysignature-collectiontumor-microenvironment
9.82 score 290 stars 216 scripts 1.9k downloads
sigminer - Extract, Analyze and Visualize Mutational Signatures for Genomic Variations
Genomic alterations including single nucleotide substitution, copy number alteration, etc. are the major force for cancer initialization and development. Due to the specificity of molecular lesions caused by genomic alterations, we can generate characteristic alteration spectra, called 'signature' (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Steele Christopher D., et al. (2022) <DOI:10.1038/s41586-022-04738-6>). This package helps users to extract, analyze and visualize signatures from genomic alteration records, thus providing new insight into cancer study.
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bayesian-nmfbioinformaticscancer-researchcnvcopynumber-signaturescosmic-signaturesdbseasy-to-useindelmutational-signaturesnmfnmf-extractionsbssignature-extractionsomatic-mutationssomatic-variantsvisualizationcpp
9.27 score 162 stars 1 dependents 214 scripts 559 downloads
UCSCXenaTools - Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
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api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
9.20 score 117 stars 1 dependents 199 scripts 1.9k downloads
UCSCXenaTools - Download and Explore Datasets from UCSC Xena Data Hubs
Download and explore datasets from UCSC Xena data hubs, which are a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others. Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
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api-clientbioinformaticsccledownloadericgctcgatoiltreehouseucscucsc-xena
9.15 score 115 stars 1 dependents 207 scripts 1.7k downloadsUCSCXenaShiny - Interactive Analysis of UCSC Xena Data
Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
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cancer-datasetshiny-appsucsc-xena
8.50 score 104 stars 87 scripts 464 downloadsUCSCXenaShiny - Interactive Analysis of UCSC Xena Data
Provides functions and a Shiny application for downloading, analyzing and visualizing datasets from UCSC Xena (<http://xena.ucsc.edu/>), which is a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
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cancer-datasetshiny-appsucsc-xena
8.50 score 104 stars 87 scripts 464 downloadsezcox - Easily Process a Batch of Cox Models
A tool to operate a batch of univariate or multivariate Cox models and return tidy result.
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batch-processingcox-model
7.72 score 23 stars 1 dependents 63 scripts 468 downloads
bregr - Easy and Efficient Batch Processing of Regression Models
Easily processes batches of univariate or multivariate regression models. Returns results in a tidy format and generates visualization plots for straightforward interpretation (Wang, Shixiang, et al. (2025) <DOI:10.1002/mdr2.70028>).
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7.33 score 15 stars 24 scripts 251 downloads
phylotaR - Automated Phylogenetic Sequence Cluster Identification from 'GenBank'
A pipeline for the identification, within taxonomic groups, of orthologous sequence clusters from 'GenBank' <https://www.ncbi.nlm.nih.gov/genbank/> as the first step in a phylogenetic analysis. The pipeline depends on a local alignment search tool and is, therefore, not dependent on differences in gene naming conventions and naming errors.
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blastngenbankpeer-reviewedphylogeneticssequence-alignment
6.07 score 25 stars 189 scripts 4 downloadscontribution - A Tiny Contribution Table Generator Based on 'ggplot2'
Contribution table for credit assignment based on 'ggplot2'. This can improve the author contribution information in academic journals and personal CV.
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contributioncreditggplot2research
5.26 score 12 stars 30 scripts 174 downloadscontribution - A Tiny Contribution Table Generator Based on 'ggplot2'
Contribution table for credit assignment based on 'ggplot2'. This can improve the author contribution information in academic journals and personal CV.
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contributioncreditggplot2research
5.26 score 12 stars 30 scripts 296 downloadsmetawho - Meta-Analytical Implementation to Identify Who Benefits Most from Treatments
A tool for implementing so called 'deft' approach (see Fisher, David J., et al. (2017) <DOI:10.1136/bmj.j573>) and model visualization.
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deft-approachmeta-analysissubgroup-analysis
4.72 score 7 stars 15 scripts 213 downloadstinyscholar - Get and Show Personal 'Google Scholar' Profile
Provides functions to get personal 'Google Scholar' profile data from web API and show it in table or figure format.
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google-scholar
4.60 score 8 stars 8 scripts 258 downloadsggpolar - Dots and Their Connections in Polar Coordinate System
Provides basic graphing functions to fully demonstrate point-to-point connections in a polar coordinate space.
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ggplot2-enhancements
4.60 score 8 stars 8 scripts 277 downloadscopynumber - Segmentation of single- and multi-track copy number data by penalized least squares regression (with hg38 and mm10).
Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.
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acghsnpcopynumbervariationgeneticsvisualization
4.03 score 21 stars 102 scriptsDoAbsolute - Automate Absolute Copy Number Calling
Provide an easy interface to automate estimation of absolute copy number, purity, ploidy using 'ABSOLUTE'.
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absolutecopy-number-variationfirehose
3.52 score 41 stars 16 scriptsregport - Regression Model Processing Port
Provides R6 classes, methods and utilities to construct, analyze, summarize, and visualize regression models.
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batch-processingregression-models
3.48 score 6 stars 3 scripts 247 downloadsIDConverter - Convert Identifiers in Biological Databases
Identifiers in biological databases connect different levels of metadata, phenotype data or genotype data. This tool is designed to easily convert identifiers within or between different biological databases (Wang, Shixiang, et al. (2021) <DOI:10.1371/journal.pgen.1009557>).
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3.10 score 9 stars 28 scripts 25 downloadssigminer.prediction - Train and Predict Cancer Subtype with Keras Model based on Mutational Signatures
Mutational signatures represent mutational processes occured in cancer evolution, thus are stable and genetic resources for subtyping. This tool provides functions for training neutral network models to predict the subtype a sample belongs to based on 'keras' and 'sigminer' packages.
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kerasmutational-signaturesprostate-cancersigminer
2.60 score 8 stars 2 scriptsneopeptides - Calculate and Explore Property Indices of Neopeptides
Includes functions to calculate and explore several property indices for neopeptides, which are abnormal peptides generated from genome.
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somaticmutationimmunooncologyalignmentimmunotherapyneoantigenpeptides
2.18 score 3 stars 2 scriptsrsra - Query and Download SRA Files from NCBI
Query and download SRA files from NCBI with 'wget'.
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2.00 score 2 stars