vimalinx/bio-agent - Page 5

gm2ranges

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

Langue du texte source : anglais

gm2segs

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

hgvs2spdi

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

hisat2-build-l

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

hisat2-extract-exons-py

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

Langue du texte source : anglais

hisat2-extract-snps-haplotypes-ucsc-py

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

Langue du texte source : anglais

hisat2-extract-snps-haplotypes-vcf-py

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

Langue du texte source : anglais

hisat2-extract-splice-sites-py

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

hisat2-inspect-s

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

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.

Langue du texte source : anglais

hisat2

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

Langue du texte source : anglais

hmmalign

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

Langue du texte source : anglais

hmmbuild

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

Langue du texte source : anglais

hmmconvert

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

Langue du texte source : anglais

hmmemit

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

hmmlogo

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

Langue du texte source : anglais

hmmpgmd-shard

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

Langue du texte source : anglais

hmmpgmd

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

Langue du texte source : anglais

hmmpress

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

Langue du texte source : anglais

hmmscan

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

Langue du texte source : anglais

hmmsearch

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

hmmstat

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

ini2xml

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

Langue du texte source : anglais

interpolate-sam-pl

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

Langue du texte source : anglais

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.

Langue du texte source : anglais

intersect-uid-lists

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

Langue du texte source : anglais

iqtree

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

Langue du texte source : anglais

iqtree3

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

Langue du texte source : anglais