vimalinx/bio-agent - 5ページ

gm2ranges

Use when converting BLAST/genomic-map alignment summaries into compact strand-and-range tables for later interval fusion.

原文の言語: 英語

gm2segs

Use when converting BLASTN mRNA alignment XML into segmented interval reports and strand-overlap summaries in EDirect pipelines.

原文の言語: 英語

group-by

Use when you need to summarize tabular data by grouping rows on common column values and applying aggregation operations (sum, count, mean, etc.), similar to SQL GROUP BY.

原文の言語: 英語

guess-ploidy-py

Use when plotting `bcftools +guess-ploidy -v` output into a PNG summary of haploid, diploid, score, and site-count signals across samples.

原文の言語: 英語

hgvs2spdi

Use when converting EDirect HGVS XML records into NCBI SPDI XML, optionally with a precomputed accession-to-CDS-offset transform table.

原文の言語: 英語

hisat2-align-l

Use when aligning RNA-seq reads to a reference genome using a HISAT2 index, particularly for splice-aware alignment of transcriptomic data.

原文の言語: 英語

hisat2-align-s

Use when aligning RNA-seq reads to a HISAT2 index using the alignment binary directly. Supports spliced alignment with optional splice site annotation.

原文の言語: 英語

hisat2-build-l

Use when building large HISAT2 index files from reference sequences for RNA-seq alignment with splice-aware mapping support.

原文の言語: 英語

hisat2-build-s

Use when building a HISAT2 graph-based index from reference sequences for splice-aware RNA-seq alignment, optionally incorporating SNPs, haplotypes, splice sites, or exon annotations.

原文の言語: 英語

hisat2-build

Use when building HISAT2 index files from reference genomes for subsequent alignment with hisat2. Handles FASTA reference inputs and creates .ht2 index files.

原文の言語: 英語

hisat2-extract-exons-py

Use when extracting exon coordinates from GTF annotation files for HISAT2 index building or splice-aware alignment preparation.

原文の言語: 英語

hisat2-extract-snps-haplotypes-ucsc-py

Use when extracting SNPs and haplotypes from UCSC SNP files for HISAT2 graph-based genome indexing.

原文の言語: 英語

hisat2-extract-snps-haplotypes-vcf-py

Use when extracting SNPs and haplotypes from VCF files to build variant-aware HISAT2 graph genome indexes

原文の言語: 英語

hisat2-extract-splice-sites-py

Use when extracting splice junctions from GTF annotation files for HISAT2 splice-aware alignment.

原文の言語: 英語

hisat2-inspect-l

Use when you need to inspect or extract information from HISAT2 large index files (.ht2l), including reference sequences, splice sites, SNPs, exons, or index summaries.

原文の言語: 英語

hisat2-inspect-s

Use when extracting metadata, reference names, SNPs, splice sites, or exon information from HISAT2 index files (.ht2).

原文の言語: 英語

hisat2-inspect

Use when you need to inspect HISAT2 index files, extract reference sequences, view index summaries, or retrieve SNP/splice site/exon information from a .ht2 index.

原文の言語: 英語

hisat2-read-statistics-py

Use when you need to compute basic read statistics (count, min/max/average length) from FASTQ/FASTA files before or after HISAT2 alignment workflows.

原文の言語: 英語

hisat2-simulate-reads-py

Use when simulating RNA-seq or DNA-seq reads from a reference genome and GTF annotation file, optionally incorporating SNP variants and controlling expression profiles.

原文の言語: 英語

hisat2

Use when aligning RNA-seq reads to a reference genome using graph-based indexing for fast and sensitive spliced alignment.

原文の言語: 英語

hmmalign

Use when aligning sequences to a profile HMM to produce multiple sequence alignments.

原文の言語: 英語

hmmbuild

Use when turning curated multiple-sequence alignments into profile HMM files for HMMER search or database-preparation workflows.

原文の言語: 英語

hmmconvert

Use when converting profile HMM files between HMMER3 ASCII or binary, legacy HMMER2, or specific 3.x text revisions.

原文の言語: 英語

hmmemit

Use when sampling synthetic sequences, alignments, or consensus sequences from one or more profile HMMs.

原文の言語: 英語

hmmfetch

Use when you need to extract specific HMM profiles from an HMM database file by name, or index an HMM file for faster lookups.

原文の言語: 英語

hmmlogo

Use when extracting per-position residue-height and indel-rate data from a profile HMM for sequence-logo visualization.

原文の言語: 英語

hmmpgmd-shard

Use when running the sharded `hmmpgmd_shard` daemon so large protein sequence databases are split across HMMER worker nodes.

原文の言語: 英語

hmmpgmd

Use when running HMMER master or worker daemon services that front `phmmer`, `hmmsearch`, and `hmmscan` against cached databases.

原文の言語: 英語

hmmpress

Use when preparing profile HMM databases for use with hmmpgmd (HMMER daemon) by creating compressed binary index files.

原文の言語: 英語

hmmscan

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

原文の言語: 英語

hmmsearch

Use when searching profile hidden Markov models against sequence databases to identify homologous sequences or protein family members

原文の言語: 英語

hmmsim

Use when you need to characterize score distributions of a profile HMM on random sequences, such as calibration checks, benchmarking, or filter-behavior experiments.

原文の言語: 英語

hmmstat

Use when you need to inspect and summarize statistics for HMM (profile hidden Markov model) files from the HMMER suite.

原文の言語: 英語

htsfile

Use when you need to identify, view, or copy HTS-format files (BAM, CRAM, VCF, BCF). Use for inspecting file headers or viewing textual representations of binary HTS files.

原文の言語: 英語

ini2xml

Use when converting INI-style configuration files into XML for downstream EDirect or XML-based processing.

原文の言語: 英語

interpolate-sam-pl

Use when deriving interpolated per-base coverage counts from a sorted SAM file, especially across paired-end inserts.

原文の言語: 英語

intersect-bed

Use when you need to find overlaps between two genomic interval files (BED, GFF, VCF, or BAM), filter features by intersection, or count/report overlapping regions between datasets.

原文の言語: 英語

intersect-uid-lists

Use when keeping only the Entrez or NCBI UIDs present in both of two UID files.

原文の言語: 英語

iqtree

Use when inferring maximum-likelihood phylogenies from aligned sequences, performing automated model selection, or assessing branch support with bootstrap or aLRT methods

原文の言語: 英語

iqtree3

Use when inferring maximum-likelihood phylogenetic trees, selecting substitution models, running bootstrap support analyses, or performing partitioned phylogenetic analyses on sequence alignments.

原文の言語: 英語