biomate-bioconductor-kb

In the author's own words, from each skill's SKILL.md — showing the first 30 of 200 files.

• bioconductor-biomart

  In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. bio

  skills/annotation/biomart/SKILL.md on GitHub (opens in a new tab)

• bioconductor-kegggraph

  KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essenti

  skills/annotation/kegggraph/SKILL.md on GitHub (opens in a new tab)

• bioconductor-enrichplot

  The 'enrichplot' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. It is mainly designed to work with the 'clusterProfiler' package suite. All the visualizati

  skills/enrichment/enrichplot/SKILL.md on GitHub (opens in a new tab)

• bioconductor-reactomepa

  Reactome is a free, open-source, curated and peer-reviewed pathway database. Their goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge.

  skills/enrichment/reactomepa/SKILL.md on GitHub (opens in a new tab)

• bioconductor-bumphunter

  Tools for finding bumps in genomic data

  skills/epigenomics/bumphunter/SKILL.md on GitHub (opens in a new tab)

• bioconductor-chipseeker

  ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p

  skills/epigenomics/chipseeker/SKILL.md on GitHub (opens in a new tab)

• bioconductor-epigrahmm

  epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. It contains two separate peak callers, one for consensus peaks from biological or technical replicates, and one for differential peaks from multi-replicate multi-condition experiments. In differential peak calling, epigraHMM provides window-specific posterior probabilities associated with every po…

  skills/epigenomics/epigrahmm/SKILL.md on GitHub (opens in a new tab)

• bioconductor-extrachips

  This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

  skills/epigenomics/extrachips/SKILL.md on GitHub (opens in a new tab)

• bioconductor-hicdcplus

  Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. The HiC-DC+ (Hi-C/HiChIP direct caller plus) package enables principled statistical analysis of Hi-C and HiChIP data sets – including calling significant interactions within a single experiment and performing differential analysis between conditions given replicate experiments – to facilitate global integrative studies…

  skills/epigenomics/hicdcplus/SKILL.md on GitHub (opens in a new tab)

• bioconductor-hicexperiment

  R generic interface to Hi-C contact matrices in `.(m)cool`, `.hic` or HiC-Pro derived formats, as well as other Hi-C processed file formats. Contact matrices can be partially parsed using a random access method, allowing a memory-efficient representation of Hi-C data in R. The `HiCExperiment` class stores the Hi-C contacts parsed from local contact matrix files. `HiCExperiment` instances can be f…

  skills/epigenomics/hicexperiment/SKILL.md on GitHub (opens in a new tab)

• bioconductor-hicontacts

  HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

  skills/epigenomics/hicontacts/SKILL.md on GitHub (opens in a new tab)

• bioconductor-macsr

  The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. This package is an R wrapper of the lastest MACS3.

  skills/epigenomics/macsr/SKILL.md on GitHub (opens in a new tab)

• bioconductor-miasim

  Microbiome time series simulation with generalized Lotka-Volterra model, Self-Organized Instability (SOI), and other models. Hubbell's Neutral model is used to determine the abundance matrix. The resulting abundance matrix is applied to (Tree)SummarizedExperiment objects.

  skills/epigenomics/miasim/SKILL.md on GitHub (opens in a new tab)

• bioconductor-minfi

  Tools to analyze & visualize Illumina Infinium methylation arrays.

  skills/epigenomics/minfi/SKILL.md on GitHub (opens in a new tab)

• bioconductor-basilisk

  Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e

  skills/general/basilisk/SKILL.md on GitHub (opens in a new tab)

• bioconductor-biobase

  Functions that are needed by many other packages or which replace R functions.

  skills/general/biobase/SKILL.md on GitHub (opens in a new tab)

• bioconductor-biovizbase

  The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and enc

  skills/general/biovizbase/SKILL.md on GitHub (opens in a new tab)

• bioconductor-dose

  This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enric

  skills/general/dose/SKILL.md on GitHub (opens in a new tab)

• bioconductor-experimenthub

  This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me

  skills/general/experimenthub/SKILL.md on GitHub (opens in a new tab)

• bioconductor-faers

  The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. faers pacakge serves as the interface between the FAERS database and R. Furthermore, faers pacakge offers a standardized approach for performing pharmacovigilance analysis.

  skills/general/faers/SKILL.md on GitHub (opens in a new tab)

• bioconductor-gdsfmt

  Provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files. GDS is portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited

  skills/general/gdsfmt/SKILL.md on GitHub (opens in a new tab)

• bioconductor-genefilter

  Some basic functions for filtering genes.

  skills/general/genefilter/SKILL.md on GitHub (opens in a new tab)

• bioconductor-geneplotter

  Functions for plotting genomic data

  skills/general/geneplotter/SKILL.md on GitHub (opens in a new tab)

• bioconductor-graphite

  Graph objects from pathway topology derived from KEGG, Panther, PathBank, PharmGKB, Reactome SMPDB and WikiPathways databases.

  skills/general/graphite/SKILL.md on GitHub (opens in a new tab)

• bioconductor-gypsum

  Client for the gypsum REST API (https://gypsum.artifactdb.com), a cloud-based file store in the ArtifactDB ecosystem. This package provides functions for uploads, downloads, and various adminstrative and management tasks. Check out the docu

  skills/general/gypsum/SKILL.md on GitHub (opens in a new tab)

• bioconductor-immunotation

  MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have b…

  skills/general/immunotation/SKILL.md on GitHub (opens in a new tab)

• bioconductor-mosbi

  This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering…

  skills/general/mosbi/SKILL.md on GitHub (opens in a new tab)

• bioconductor-multiassayexperiment

  Harmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of st

  skills/general/multiassayexperiment/SKILL.md on GitHub (opens in a new tab)

• bioconductor-pcamethods

  Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA o

  skills/general/pcamethods/SKILL.md on GitHub (opens in a new tab)

• bioconductor-qvalue

  This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false

  skills/general/qvalue/SKILL.md on GitHub (opens in a new tab)

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