vimalinx/bio-agent - Seite 7

pair-to-bed

Use when you need to find overlaps between paired-end read intervals (BEDPE or BAM) and genomic features in BED, GFF, or VCF format.

Quellsprache: Englisch

pair-to-pair

Use when comparing two paired-end BEDPE files to find overlapping pairs. Requires -a and -b BEDPE input files.

Quellsprache: Englisch

phage-design

Use when working from the local Evo 2 `phage_gen` project to design or analyze bacteriophage genomes, competition assays, or Gibson assembly fragments.

Quellsprache: Englisch

phmmer

Use when searching one or more protein query sequences against a protein sequence database with HMMER's one-pass sequence-vs-sequence searcher.

Quellsprache: Englisch

plot-ampliconstats

Use when visualizing amplicon sequencing statistics from samtools ampliconstats output, generating heatmaps and graphs for coverage and read analysis.

Quellsprache: Englisch

plot-bamstats

Use when visualizing `samtools stats` output as BAM QC plots, including merged reports and reference-GC-aware summaries.

Quellsprache: Englisch

plot-roh-py

Use when plotting runs of homozygosity from `run-roh.pl` style output directories into PNG tracks, optionally filtered by region, sample list, or group contrast.

Quellsprache: Englisch

plot-vcfstats

Use when converting `bcftools stats` output into variant-QC plots, per-sample PNG panels, and optional PDF summaries.

Quellsprache: Englisch

pma2apa

Use when converting `PubmedArticle` XML from EDirect into APA-style citation text or APA-structured XML for downstream parsing.

Quellsprache: Englisch

pma2pme

Use when converting `PubmedArticle` XML into `Pubmed-entry` ASN.1 text, or into the intermediate XML form used before final ASN.1 emission.

Quellsprache: Englisch

pmc2bioc

Use when converting PubMed Central article XML into BioC collection XML for downstream text-mining or annotation pipelines.

Quellsprache: Englisch

pmc2info

Use when converting PubMed Central article XML into normalized PMCInfo XML for local archive building or section-aware downstream parsing.

Quellsprache: Englisch

popt

Use when filtering `RNAsubopt -s` output to keep p-optimal RNA structures in a ViennaRNA post-processing pipeline.

Quellsprache: Englisch

print-columns

Use when projecting or transforming tab-delimited stdin columns with a tiny EDirect `awk` wrapper, especially for quick field arithmetic, quoting, or date stamping in shell pipelines.

Quellsprache: Englisch

print-missing-subranges

Use when reporting gaps in an ordered list of ascending integer positions, identifiers, or coordinates by printing the missing ranges between observed values.

Quellsprache: Englisch

prodigal

Use when predicting protein-coding genes in prokaryotic genomes or metagenomic sequences

Quellsprache: Englisch

project-tree-builder

Use when generating or dry-running NCBI-style Unix C++ project trees with `project_tree_builder`.

Quellsprache: Englisch

propmapped

Use when you need to calculate the proportion of mapped reads or fragments from SAM/BAM alignment files to assess mapping quality and success rates.

Quellsprache: Englisch

protein-structure

Use when planning or staging protein-structure prediction or structure-design work in this workspace, especially when deciding between missing local predictors and the repos that are actually present.

Quellsprache: Englisch

psiblast

Use when detecting distant protein homologs via iterative profile-based searches, building position-specific scoring matrices (PSSMs), or refining sequence similarity searches beyond standard BLASTP.

Quellsprache: Englisch

psl2sam-pl

Use when converting UCSC PSL alignments into SAM and controlling the simple alignment score calculation.

Quellsprache: Englisch

qualfa2fq-pl

Use when merging a legacy FASTA file and matching QUAL file into FASTQ, including `.gz` inputs, before downstream alignment or QC steps.

Quellsprache: Englisch

quality-scores

Use when sampling per-base Phred quality values from FASTQ, gzipped FASTQ, BAM, or SAM files via the Subread `qualityScores` utility.

Quellsprache: Englisch

quote-grouped-elements

Use when converting space-separated grouped values into quoted comma-joined lines for downstream EDirect or shell formatting steps.

Quellsprache: Englisch

random-bed

Use when generating random genomic intervals for simulation, background sets, or statistical testing.

Quellsprache: Englisch

rchive-linux

Use when calling the Linux-specific compiled `rchive.Linux` binary directly to build, query, or manage local XML archives and postings indices.

Quellsprache: Englisch

rchive

Use when building, indexing, or querying local XML record archives from NCBI Entrez databases, creating inverted indices, or managing PubMed local caches.

Quellsprache: Englisch

ref-cache

Use when managing local reference sequence caches for htslib-based tools. Invokes the ref-cache CLI to configure or interact with reference cache directories.

Quellsprache: Englisch

ref2pmid

Use when converting reference citations or identifiers to PubMed IDs (PMIDs) using Entrez Direct utilities.

Quellsprache: Englisch

refseq-nm-cds

Use when retrieving RefSeq NM coding sequences for supported species (cow, frog, human, mouse, pig, rat, zebrafish) via the entrez-direct toolkit.

Quellsprache: Englisch

remove-dup

Use when removing duplicate alignments from SAM or BAM files with the Subread `removeDup` CLI and a location-count cutoff.

Quellsprache: Englisch

reorder-columns

Use when you need to reorder columns in tabular bioinformatics data files while preserving row content.

Quellsprache: Englisch

repair

Use when paired-end reads need to be reordered so mates appear consecutively, or when preparing BAM files for featureCounts by adding dummy reads for singletons.

Quellsprache: Englisch

rfdiffusion

Use when working from the local RFdiffusion repository to generate protein backbones or binder designs through its Docker Compose workflows.

Quellsprache: Englisch

rna2-dfold

Use when computing MFE structures, partition functions, and Boltzmann-sampled secondary structures within k,l distance neighborhoods relative to two reference structures for an RNA sequence.

Quellsprache: Englisch

rnaaliduplex

Use when predicting conserved RNA-RNA interactions between two CLUSTAL alignments to identify evolutionary conserved binding sites, hybridization energies, and duplex structures.

Quellsprache: Englisch

rnaalifold

Use when predicting consensus secondary structures from multiple sequence alignments of RNA. Computes minimum free energy structures, partition functions, and base pairing probabilities for aligned RNA sequences.

Quellsprache: Englisch

rnacofold

Use when predicting secondary structures of two RNA sequences with dimerization, computing equilibrium concentrations of monomer and dimer species, or analyzing RNA-RNA hybridization thermodynamics.

Quellsprache: Englisch

rnaconsensus

Use when predicting RNA secondary structures for single sequences using information from multiple sequence alignments of homologous sequences.

Quellsprache: Englisch

rnadistance

Use when calculating distances between RNA secondary structures, including base pair distance and tree or string editing-based dissimilarity measures.

Quellsprache: Englisch