Menu
Skills dans ce dépôt
SkillsMP a collecté 417 skills depuis vimalinx/bio-agent. Ouvrez un skill pour examiner sa source et ses détails.
vimalinx/bio-agentAffichage de 40 skills collectés sur 417.
Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.
Langue du texte source : anglais
Use when smoke-testing an Entrez Direct installation with the bundled long-form example suite or the focused `-test` trace mode.
Langue du texte source : anglais
Use when probing NCBI E-utilities reachability or endpoint health with the bundled `-alive`, `-all`, or per-endpoint diagnostic checks.
Langue du texte source : anglais
Use when testing or benchmarking PCRE2 regular expressions with the local `test_pcre` / `pcre2test` executable.
Langue du texte source : anglais
Use when validating a local PMC archive/index configured through `EDIRECT_LOCAL_ARCHIVE` by round-tripping random PMC records through `xfetch` and `xsearch`.
Langue du texte source : anglais
Use when validating a local PubMed archive/postings installation configured through `EDIRECT_LOCAL_ARCHIVE` and related local EDirect helpers.
Langue du texte source : anglais
Use when converting TOML configuration or metadata files into XML for downstream EDirect or XML-based processing.
Langue du texte source : anglais
Use when calling the Linux-specific compiled `transmute.Linux` binary directly for NCBI format conversion, sequence processing, or variation-processing workflows.
Langue du texte source : anglais
Use when invoking the public `transmute` wrapper for format conversion, sequence editing, or shell-level helper modes that may be intercepted before dispatch to the platform binary.
Langue du texte source : anglais
Use when you need to align multiple bedGraph tracks onto a shared interval segmentation so their values can be compared side by side.
Langue du texte source : anglais
Use when removing invariant columns from a tab-delimited table, especially in EDirect or bioinformatics comparison pipelines.
Langue du texte source : anglais
Use when downloading or updating pre-formatted BLAST databases from NCBI or cloud providers (AWS, GCP)
Langue du texte source : anglais
Use when annotating VCF files with custom annotations, applying filters, or modifying INFO/ID/QUAL/FILTER columns.
Langue du texte source : anglais
Use when comparing two or more bgzipped and tabix-indexed VCF files to assess concordance of variant calls, positions, or genotypes.
Langue du texte source : anglais
Use when concatenating VCF files split by chromosome or when merging multiple gzipped VCFs into a single output.
Langue du texte source : anglais
Use when applying VCF variants to a reference FASTA to generate a consensus sequence.
Langue du texte source : anglais
Use when comparing variant samples against background samples to identify unique genotypes and novel variants in VCF files.
Langue du texte source : anglais
Use when converting VCF files between format versions (4.0, 4.1, 4.2) for compatibility with downstream bioinformatics tools.
Langue du texte source : anglais
Use when VCF files have inconsistent or non-native newline characters and need normalization before downstream processing.
Langue du texte source : anglais
Use when VCF files have incorrect ploidy annotations for sex chromosomes or mitochondrial DNA, particularly when processing samples with known sex but mismatched genotype fields.
Langue du texte source : anglais
Use when calculating in-frame indel ratios from VCF files, optionally with exon annotations.
Langue du texte source : anglais
Use when you need to compute intersections, unions, or complements between bgzipped and tabix-indexed VCF or tab-delimited files.
Langue du texte source : anglais
Use when merging multiple VCF files by genomic position to create multi-sample VCFs from individual or fewer-sample VCFs.
Langue du texte source : anglais
Use when joining multiple overlapping pre-phased VCF chunks into a single phased VCF using heterozygous calls from overlaps to determine correct phase.
Langue du texte source : anglais
Use when extracting and formatting specific fields from compressed VCF files, querying variants by region, or generating custom tabular output with genotype and INFO data.
Langue du texte source : anglais
Use when you need to reorder sample columns in a VCF file to match the column order of a template VCF.
Langue du texte source : anglais
Use when VCF files need sorting by chromosome and position, particularly before downstream analysis or indexing. Pipes VCF input through stdin.
Langue du texte source : anglais
Use when computing statistics on VCF files, filtering variant data by quality or fields, or generating summary reports from gzipped VCF inputs.
Langue du texte source : anglais
Use when subsetting VCF files by samples or filtering variant types from bgzipped VCF input.
Langue du texte source : anglais
Use when converting VCF genotype data to simple tabular format for downstream analysis or reporting.
Langue du texte source : anglais
Use when you need to calculate the transition/transversion (Ts/Tv) ratio from VCF files for variant call quality assessment.
Langue du texte source : anglais
Use when you need to validate VCF files for format compliance and detect issues like duplicate positions.
Langue du texte source : anglais
Use when working with Variant Call Format (VCF) files and need to filter, summarize, or manipulate variant data.
Langue du texte source : anglais
Use when working with VCF file utilities from the bcftools bioconda package.
Langue du texte source : anglais
Use when summarizing `bcftools +vrfs`/`vrfs` `SITE` output into selected sites or variance vectors from a subset of loci.
Langue du texte source : anglais
Use when evaluating wgsim simulation results or analyzing simulated read data as part of samtools bioconda installations.
Langue du texte source : anglais
Use when simulating paired-end short reads from a reference FASTA for testing, benchmarking, or pipeline validation
Langue du texte source : anglais
Use when you need to find features in one file that fall within a configurable window around features in another file, including strand-aware upstream and downstream proximity searches.
Langue du texte source : anglais
Use when you need to create adjacent or sliding windows across a genome or BED file for binning genomic regions into fixed-size or fixed-count intervals.
Langue du texte source : anglais
Use when adapting or converting WindowMasker output files for compatibility with different BLAST pipeline versions or formats.
Langue du texte source : anglais