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O SkillsMP coletou 200 skills de bioMate-AI/biomate-bioconductor-kb. Abra uma skill para revisar a origem e os detalhes.
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Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various
Idioma do texto original: inglês
algorithm for determining cluster count and membership by stability evidence in unsupervised analysis
Idioma do texto original: inglês
A toolset for deciphering and managing biological sequences.
Idioma do texto original: inglês
Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.
Idioma do texto original: inglês
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD);…
Idioma do texto original: inglês
Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual…
Idioma do texto original: inglês
Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working wit
Idioma do texto original: inglês
Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a
Idioma do texto original: inglês
The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose
Idioma do texto original: inglês
The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor
Idioma do texto original: inglês
Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. The "ggmanh" package aims to keep the generation of these plots simple while maintaining customizability. Main functions include manhattan_plot, qqunif,…
Idioma do texto original: inglês
'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics. 'ggtree' is designed for visualization and annotation of phylogenetic trees and other tree-like structures with their annotation data.
Idioma do texto original: inglês
The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R packag
Idioma do texto original: inglês
Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to
Idioma do texto original: inglês
A package that provides a client interface to the Kyoto Encyclopedia of Genes and Genomes (KEGG) REST API. Only for academic use by academic users belonging to academic institutions (see <https://www.kegg.jp/kegg/rest/>). Note that KEGGREST
Idioma do texto original: inglês
When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to…
Idioma do texto original: inglês
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to…
Idioma do texto original: inglês
The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.
Idioma do texto original: inglês
Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. This work was partially supported by grant no. R21HG005912 from the National Human Genome Research Institute.
Idioma do texto original: inglês
This package provides an interface to the 'samtools', 'bcftools', and 'tabix' utilities for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.
Idioma do texto original: inglês
Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/imp
Idioma do texto original: inglês
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, an
Idioma do texto original: inglês
Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology…
Idioma do texto original: inglês
syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. Anchor pairs are detected with the MCScanX algorithm, which was ported to this package with the Rcpp framework for R and C++ integration. Anchor pairs from…
Idioma do texto original: inglês
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It c
Idioma do texto original: inglês
A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and
Idioma do texto original: inglês
This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. The cytoviewer interface is divided into image-level (Composite…
Idioma do texto original: inglês
EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. Thi
Idioma do texto original: inglês
Provides S4 data structures and basic functions to deal with flow cytometry data.
Idioma do texto original: inglês
lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data…
Idioma do texto original: inglês
The R implementation for the Grammar of Succint Lipid Nomenclature parses different short hand notation dialects for lipid names. It normalizes them to a standard name. It further provides calculated monoisotopic masses and sum formulas for each successfully…
Idioma do texto original: inglês
This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limi
Idioma do texto original: inglês
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed fu
Idioma do texto original: inglês
Utilities for microbiome analysis.
Idioma do texto original: inglês
phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.
Idioma do texto original: inglês
The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. Experimental methods supported include dynamic LOPIT-DC, hyperLOPIT, Dynamic Organellar Maps, Dynamic PCP. It provides…
Idioma do texto original: inglês
the R package BioNAR, developed to step by step analysis of PPI network. The aim is to quantify and rank each protein’s simultaneous impact into multiple complexes based on network topology and clustering. Package also enables estimating of co-occurrence of…
Idioma do texto original: inglês
Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. The required drug-target interaction information is obained from a local SQLite instance of the ChEMBL database. ChEMBL has been chosen for…
Idioma do texto original: inglês
Data quality assessment is an integral part of preparatory data analysis to ensure sound biological information retrieval. We present here the MatrixQCvis package, which provides shiny-based interactive visualization of data quality metrics at the per-sample…
Idioma do texto original: inglês
Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducin
Idioma do texto original: inglês