vimalinx/bio-agent - 5페이지

gm2ranges

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

원문 언어: 영어

gm2segs

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

원문 언어: 영어

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.

원문 언어: 영어

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.

원문 언어: 영어

hgvs2spdi

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

원문 언어: 영어

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.

원문 언어: 영어

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.

원문 언어: 영어

hisat2-build-l

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

원문 언어: 영어

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.

원문 언어: 영어

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.

원문 언어: 영어

hisat2-extract-exons-py

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

원문 언어: 영어

hisat2-extract-snps-haplotypes-ucsc-py

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

원문 언어: 영어

hisat2-extract-snps-haplotypes-vcf-py

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

원문 언어: 영어

hisat2-extract-splice-sites-py

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

원문 언어: 영어

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.

원문 언어: 영어

hisat2-inspect-s

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

원문 언어: 영어

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.

원문 언어: 영어

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.

원문 언어: 영어

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.

원문 언어: 영어

hisat2

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

원문 언어: 영어

hmmalign

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

원문 언어: 영어

hmmbuild

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

원문 언어: 영어

hmmconvert

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

원문 언어: 영어

hmmemit

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

원문 언어: 영어

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.

원문 언어: 영어

hmmlogo

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

원문 언어: 영어

hmmpgmd-shard

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

원문 언어: 영어

hmmpgmd

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

원문 언어: 영어

hmmpress

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

원문 언어: 영어

hmmscan

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

원문 언어: 영어

hmmsearch

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

원문 언어: 영어

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.

원문 언어: 영어

hmmstat

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

원문 언어: 영어

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.

원문 언어: 영어

ini2xml

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

원문 언어: 영어

interpolate-sam-pl

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

원문 언어: 영어

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.

원문 언어: 영어

intersect-uid-lists

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

원문 언어: 영어

iqtree

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

원문 언어: 영어

iqtree3

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

원문 언어: 영어