bioMate-AI/biomate-bioconductor-kb
Skill Claude CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
'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 CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
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 CodeCodex
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.
Skill Claude CodeCodex
Run real bioinformatics, drug-discovery, and clinical workflows on BioMate's BioMate cloud infrastructure. Use whenever the user asks to screen compounds (ADMET, docking), analyze sequencing data (RNA-seq, WGS, variant calling), reconstruct cryo-EM, model PK/PBPK, predict protein structure, or generate IND / CRO…