bioMate-AI/biomate-bioconductor-kb

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 manhattanplot, qqunif, and thinPoints.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

'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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 ). Note that KEGGREST.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 reference sequence and generate scar form strings respectively.…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 any scoring for DNA or AA characters. E.g. by using literal…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 is based on the one described in Afsari (2021, ELife).

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Infer a global synteny network from multiple proteomes, cluster it, perform phylogenomic profiling, and reconstruct a microsynteny-based phylogeny.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 and Channels) and cell-level visualization (Masks). It allows…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Provides S4 data structures and basic functions to deal with flow cytometry data.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

Simultaneously calculate LISA curves, perform k-means clustering, and visualize the identified tissue regions and cell-type enrichments.

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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 parsed lipid name and supplements it with LIPID MAPS…

bioMate-AI/biomate-bioconductor-kb

Skill Claude Code

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.