vimalinx/bio-agent - 8ページ

rnados

Use when summarizing an RNA folding landscape by counting how many structures fall into each energy band, rather than enumerating individual folds one by one.

原文の言語: 英語

rnaduplex

Use when computing optimal and suboptimal secondary structures for hybridization of two RNA strands, such as probe-target binding predictions.

原文の言語: 英語

rnaeval

Use when evaluating the free energy (kcal/mol) of an RNA secondary structure, calculating co-folding energies for two RNA strands, or analyzing consensus structures from multiple sequence alignments.

原文の言語: 英語

rnafold

Use when predicting RNA secondary structures, calculating minimum free energy (MFE) folds, or computing partition functions and base pairing probabilities for RNA sequences.

原文の言語: 英語

rnaforester

Use when comparing, aligning, or computing similarity/distance between RNA secondary structures, or when generating multiple structure alignments with consensus prediction.

原文の言語: 英語

rnaheat

Use when computing RNA specific heat profiles from sequence data to analyze melting behavior and thermal stability across temperature ranges.

原文の言語: 英語

rnainverse

Use when searching for RNA sequences that fold into a predefined secondary structure, inverting RNA folding predictions to find sequences matching target bracket notation structures.

原文の言語: 英語

rnalalifold

Use when predicting locally stable secondary structures from multiple sequence alignments of RNA

原文の言語: 英語

rnalfold

Use when computing locally stable RNA secondary structures with a maximal base pair span, scanning large genomes for short RNA structures, or predicting local RNA folding with Z-score filtering.

原文の言語: 英語

rnalocmin

Use when analyzing RNA secondary structure landscapes to find local minima via gradient walks, generate barrier trees, or compute rates for kinetic modeling with treekin.

原文の言語: 英語

rnamultifold

Use when predicting secondary structures and base pairing probabilities for multiple interacting RNA molecules

原文の言語: 英語

rnapaln

Use when performing pairwise structural alignments of RNA sequences that incorporate both sequence and structure information through base pair propensity vectors.

原文の言語: 英語

rnaparconv

Use when converting legacy ViennaRNA 1.8.4 energy parameter files to the 2.0+ format used by modern ViennaRNA tools.

原文の言語: 英語

rnapdist

Use when calculating structure distances between thermodynamic ensembles of RNA secondary structures from sequence input.

原文の言語: 英語

rnapkplex

Use when searching an RNA sequence for pseudoknot-forming interactions by combining local accessibility with interaction energy, especially when ordinary pseudoknot-free folding is insufficient.

原文の言語: 英語

rnaplex

Use when screening a small query RNA against longer target RNA sequences for inter-molecular hybridization sites, especially when optional RNAplfold accessibility profiles should influence the ranking.

原文の言語: 英語

rnaplfold

Use when computing local RNA secondary structure pair probabilities, scanning large genomes for short stable RNA structures, or analyzing unpaired region probabilities across sliding windows.

原文の言語: 英語

rnaplot

Use when visualizing RNA secondary structures from dot-bracket notation or Stockholm alignments, generating structure diagrams, or creating annotated consensus structure plots.

原文の言語: 英語

rnapvmin

Use when working with RNA soft constraints and need to compute pairing probabilities with position-specific perturbation minimization from the ViennaRNA package.

原文の言語: 英語

rnaseq-pipeline

Use when building or reviewing an end-to-end RNA-seq workflow from raw reads through quantification, differential expression, and basic interpretation.

原文の言語: 英語

rnasnoop

Use when searching target RNAs for interactions with a query H/ACA snoRNA, especially when the search should respect H/ACA-specific structural constraints and optionally use accessibility profiles.

原文の言語: 英語

rnasubopt

Use when computing suboptimal RNA secondary structures within an energy range above the minimum free energy, or when sampling structures from the Boltzmann ensemble.

原文の言語: 英語

rnaup

Use when calculating thermodynamics of RNA-RNA interactions, including accessibility and binding energy predictions for RNA duplex formation.

原文の言語: 英語

roh-viz

Use when turning `bcftools roh` output plus a VCF/BCF into an interactive HTML visualization of ROH segments and homozygosity rates.

原文の言語: 英語

rpsblast

Use when searching protein sequences against conserved domain databases like CDD using reverse position-specific BLAST

原文の言語: 英語

rpstblastn

Use when searching nucleotide sequences against protein domain profile databases (PSSMs) to detect conserved domains via position-specific scoring.

原文の言語: 英語

run-ncbi-converter

Use when launching an NCBI converter binary through the `run-ncbi-converter` wrapper that downloads and caches the platform-specific executable on demand.

原文の言語: 英語

run-roh-pl

Use when batch-running `bcftools roh` across a directory of VCF, VCF.GZ, or BCF files and merging the resulting ROH calls across samples.

原文の言語: 英語

run-with-lock

Use when wrapping a command in NCBI-style file locking so only one worker for a given lock base runs at a time.

原文の言語: 英語

sam2vcf-pl

Use when converting old `samtools pileup -c` output into VCF and filtering for SNP-only or indel-only calls.

原文の言語: 英語

samtools-pl

Use when working with samtools.pl, a Perl CLI utility installed by the bioconda samtools package.

原文の言語: 英語

samtools

Use when working with SAM, BAM, or CRAM alignment files to sort, index, view, convert, or compute statistics.

原文の言語: 英語

scn2xml

Use when converting SCN-format records into XML for downstream EDirect or XML-based processing.

原文の言語: 英語

segmasker

Use when identifying and masking low-complexity regions in protein sequences with the SEG algorithm before BLAST or other downstream analyses.

原文の言語: 英語

seq-cache-populate-pl

Use when populating an htslib/CRAM `REF_CACHE` directory from FASTA input or by scanning a directory tree for FASTA files.

原文の言語: 英語

seqkit

Use when working with FASTA or FASTQ files for statistics, filtering, transformation, format conversion, searching, or set operations.

原文の言語: 英語

seqtk

Use when doing lightweight FASTA/FASTQ transformations such as conversion, subsampling, subsequence extraction, trimming, or quick QC with seqtk.

原文の言語: 英語

sequence-analysis

Use when routing DNA, RNA, or protein sequence tasks to the core sequence-analysis commands that are actually installed in this workspace.

原文の言語: 英語

shift-bed

Use when you need to shift genomic intervals in BED/GFF/VCF files by a specified number of base pairs, either uniformly or strand-specifically.

原文の言語: 英語

shuffle-bed

Use when you need to randomly permute feature locations across a genome for statistical testing or generating null distributions.

原文の言語: 英語