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bioconductor-rnaseqsamplesizedata
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public |
RnaSeqSampleSizeData
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2025-04-22 |
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r-sequenza
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public |
Tools to analyze genomic sequencing data from paired normal-tumor samples, including cellularity and ploidy estimation; mutation and copy number (allele-specific and total copy number) detection, quantification and visualization.
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2025-04-22 |
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bioconductor-targetscan.hs.eg.db
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public |
TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.
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2025-04-22 |
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bioconductor-enrichplot
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public |
Visualization of Functional Enrichment Result
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2025-04-22 |
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r-gpca
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public |
This package implements guided principal components analysis for the detection of batch effects in high-throughput data.
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2025-04-22 |
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r-poppr
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public |
An R package for genetic analysis of populations with mixed (clonal/sexual) reproduction
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2025-04-22 |
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r-polysat
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public |
A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes.
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2025-04-22 |
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r-fgwas
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public |
GWAS tools for longitudinal genetic traits based on fGWAS statistical model.
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2025-04-22 |
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bioconductor-delayedmatrixstats
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public |
Functions that Apply to Rows and Columns of 'DelayedMatrix' Objects
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2025-04-22 |
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purge_haplotigs
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public |
Pipeline to help with curating heterozygous diploid genome assemblies.
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2025-04-22 |
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r-metstat
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public |
A diverse collection of metabolomics related statistical tools.
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2025-04-22 |
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r-popgenome
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public |
Provides efficient tools for population genomics data analysis, able to process individual loci, large sets of loci, or whole genomes. PopGenome <DOI:10.1093/molbev/msu136> not only implements a wide range of population genetics statistics, but also facilitates the easy implementation of new algorithms by other researchers. PopGenome is optimized for speed via the seamless integration of C code.
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2025-04-22 |
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r-blockfest
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public |
An R implementation of an extension of the 'BayeScan' software (Foll, 2008) <DOI:10.1534/genetics.108.092221> for codominant markers, adding the option to group individual SNPs into pre-defined blocks. A typical application of this new approach is the identification of genomic regions, genes, or gene sets containing one or more SNPs that evolved under directional selection.
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2025-04-22 |
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r-whopgenome
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public |
Provides very fast access to whole genome, population scale variation data from VCF files and sequence data from FASTA-formatted files. It also reads in alignments from FASTA, Phylip, MAF and other file formats. Provides easy-to-use interfaces to genome annotation from UCSC and Bioconductor and gene ontology data from AmiGO and is capable to read, modify and write PLINK .PED-format pedigree files.
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2025-04-22 |
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bioconductor-elmer
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public |
Inferring Regulatory Element Landscapes and Transcription Factor Networks Using Cancer Methylomes
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2025-04-22 |
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bioconductor-elmer.data
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public |
Data for the ELMER package
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2025-04-22 |
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r-fastqcr
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public |
'FASTQC' is the most widely used tool for evaluating the quality of high throughput sequencing data. It produces, for each sample, an html report and a compressed file containing the raw data. If you have hundreds of samples, you are not going to open up each 'HTML' page. You need some way of looking at these data in aggregate. 'fastqcr' Provides helper functions to easily parse, aggregate and analyze 'FastQC' reports for large numbers of samples. It provides a convenient solution for building a 'Multi-QC' report, as well as, a 'one-sample' report with result interpretations.
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2025-04-22 |
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bioconductor-hiccompare
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public |
HiCcompare: Joint normalization and comparative analysis of multiple Hi-C datasets
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2025-04-22 |
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bioconductor-zinbwave
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public |
Zero-Inflated Negative Binomial Model for RNA-Seq Data
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2025-04-22 |
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r-ggrasp
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public |
Given a group of genomes and their relationship with each other, the package clusters the genomes and selects the most representative members of each cluster. Additional data can be provided to the prioritize certain genomes. The results can be printed out as a list or a new phylogeny with graphs of the trees and distance distributions also available. For detailed introduction see: Thomas H Clarke, Lauren M Brinkac, Granger Sutton, and Derrick E Fouts (2018), GGRaSP: a R-package for selecting representative genomes using Gaussian mixture models, Bioinformatics, bty300, <doi:10.1093/bioinformatics/bty300>.
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2025-04-22 |
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r-coenocliner
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public |
Simulate species occurrence and abundances (counts) along gradients.
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2025-04-22 |
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r-phylosignal
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public |
A collection of tools to explore the phylogenetic signal in univariate and multivariate data. The package provides functions to plot traits data against a phylogenetic tree, different measures and tests for the phylogenetic signal, methods to describe where the signal is located and a phylogenetic clustering method.
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2025-04-22 |
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r-phylomeasures
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public |
Given a phylogenetic tree T and an assemblage S of species represented as a subset of tips in T, we want to compute a measure of the diversity of the species in S with respect to T. The current package offers efficient algorithms that can process large phylogenetic data for several such measures. Most importantly, the package includes algorithms for computing efficiently the standardized versions of phylogenetic measures and their p-values, which are essential for null model comparisons. Among other functions, the package provides efficient computation of richness-standardized versions for indices such as the net relatedness index (NRI), nearest taxon index (NTI), phylogenetic diversity index (PDI), and the corresponding indices of two-sample measures. The package also introduces a new single-sample measure, the Core Ancestor Cost (CAC); the package provides functions for computing the value and the standardised index of the CAC and, more than that, there is an extra function available that can compute exactly any statistical moment of the measure. The package supports computations under different null models, including abundance-weighted models.
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2025-04-22 |
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r-bipartite
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public |
Functions to visualise webs and calculate a series of indices commonly used to describe pattern in (ecological) webs. It focuses on webs consisting of only two levels (bipartite), e.g. pollination webs or predator-prey-webs. Visualisation is important to get an idea of what we are actually looking at, while the indices summarise different aspects of the web's topology.
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2025-04-22 |
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r-kinship2
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public |
Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria, and kinship for the X chromosome.
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2025-04-22 |
