swaruplab/operon - 第 8 页

ribo-seq-orf-detection

Detect and quantify translated ORFs from Ribo-seq data including uORFs and novel ORFs using RiboCode and ORFquant. Use when identifying translated regions beyond annotated coding sequences or quantifying ORF-level translation.

原文语言：英语

ribo-seq-riboseq-preprocessing

Preprocess ribosome profiling data including adapter trimming, size selection, rRNA removal, and alignment. Use when preparing Ribo-seq reads for downstream analysis of translation.

原文语言：英语

ribo-seq-ribosome-periodicity

Validate Ribo-seq data quality by checking 3-nucleotide periodicity and calculating P-site offsets. Use when assessing library quality or determining read offsets for downstream analysis.

原文语言：英语

ribo-seq-ribosome-stalling

Detect ribosome pausing and stalling sites from Ribo-seq data at codon resolution. Use when studying translational regulation, identifying pause sites, or analyzing codon-specific translation dynamics.

原文语言：英语

ribo-seq-translation-efficiency

Calculate translation efficiency (TE) as the ratio of ribosome occupancy to mRNA abundance. Use when comparing translational regulation between conditions or identifying genes with altered translation independent of transcription.

原文语言：英语

rna-quantification-alignment-free-quant

Quantify transcript expression using pseudo-alignment with Salmon or kallisto. Use when quantifying transcripts with Salmon or kallisto.

原文语言：英语

rna-quantification-count-matrix-qc

Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships. Use when assessing count matrix quality before DE analysis.

原文语言：英语

rna-quantification-featurecounts-counting

Count reads per gene from aligned BAM files using Subread featureCounts. Use when processing BAM files from STAR/HISAT2 to generate gene-level counts for DESeq2/edgeR.

原文语言：英语

rna-quantification-tximport-workflow

Import transcript-level quantifications from Salmon/kallisto into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when importing transcript counts into R for DESeq2/edgeR.

原文语言：英语

rna-structure-ncrna-search

Searches for non-coding RNA homologs and classifies RNA families using Infernal covariance model searches against the Rfam database. Identifies structured RNAs by sequence and secondary structure conservation. Use when querying sequences against Rfam,…

原文语言：英语

rna-structure-secondary-structure-prediction

Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold). Computes base-pair probabilities, centroid structures, and consensus structures from alignments. Use when…

原文语言：英语

rna-structure-structure-probing

Analyzes experimental RNA structure probing data from SHAPE-MaP and DMS-MaPseq experiments using ShapeMapper2. Converts mutation rates to per-nucleotide reactivity profiles that constrain structure prediction. Use when processing SHAPE-MaP or DMS-MaPseq…

原文语言：英语

batch-processing

Process multiple sequence files in batch using Biopython. Use when working with many files, merging/splitting sequences, or automating file operations across directories.

原文语言：英语

compressed-files

Read and write compressed sequence files (gzip, bzip2, BGZF) using Biopython. Use when working with .gz or .bz2 sequence files. Use BGZF for indexable compressed files.

原文语言：英语

fastq-quality

Work with FASTQ quality scores using Biopython. Use when analyzing read quality, filtering by quality, trimming low-quality bases, or generating quality reports.

原文语言：英语

filter-sequences

Filter and select sequences by criteria (length, ID, GC content, patterns) using Biopython. Use when subsetting sequences, removing unwanted records, or selecting by specific criteria.

原文语言：英语

format-conversion

Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when changing file formats or preparing data for different tools.

原文语言：英语

paired-end-fastq

Handle paired-end FASTQ files (R1/R2) using Biopython. Use when working with Illumina paired reads, synchronizing pairs, interleaving/deinterleaving, or filtering paired data.

原文语言：英语

read-sequences

Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) using Biopython Bio.SeqIO. Use when parsing sequence files, iterating multi-sequence files, random access to large files, or high-performance parsing.

原文语言：英语

sequence-statistics

Calculate sequence statistics (N50, length distribution, GC content, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing assemblies.

原文语言：英语

write-sequences

Write biological sequences to files (FASTA, FASTQ, GenBank, EMBL) using Biopython Bio.SeqIO. Use when saving sequences, creating new sequence files, or outputting modified records.

原文语言：英语

codon-usage

Analyze codon usage, calculate CAI (Codon Adaptation Index), and examine synonymous codon bias using Biopython. Use when analyzing coding sequences for expression optimization or evolutionary analysis.

原文语言：英语

motif-search

Find patterns, motifs, and subsequences in biological sequences using Biopython. Use when searching for transcription factor binding sites, regulatory elements, or any sequence pattern. For restriction enzyme analysis, use the restriction-analysis skill.

原文语言：英语

reverse-complement

Generate reverse complements and complements of DNA/RNA sequences using Biopython. Use when working with opposite strands, primer design, or converting between template and coding strands.

原文语言：英语

seq-objects

Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, or building annotated sequence records.

原文语言：英语

sequence-properties

Calculate sequence properties like GC content, molecular weight, isoelectric point, and GC skew using Biopython. Use when analyzing sequence composition, computing physical properties, or comparing sequences.

原文语言：英语

sequence-slicing

Slice, extract, and concatenate biological sequences using Biopython. Use when extracting subsequences, joining sequences, or manipulating sequence regions by position.

原文语言：英语

transcription-translation

Transcribe DNA to RNA and translate to protein using Biopython. Use when converting between DNA, RNA, and protein sequences, finding ORFs, or using alternative codon tables.

原文语言：英语

small-rna-seq-differential-mirna

Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations. Use when identifying miRNAs that change between treatment groups, disease states, or developmental stages.

原文语言：英语

small-rna-seq-mirdeep2-analysis

Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data. Use when identifying new miRNAs or performing comprehensive miRNA profiling with discovery.

原文语言：英语

small-rna-seq-mirge3-analysis

Fast miRNA quantification with isomiR detection and A-to-I editing analysis using miRge3. Use when quantifying known miRNAs quickly or analyzing isomiR variants and RNA editing.

原文语言：英语

small-rna-seq-smrna-preprocessing

Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs. Use when preparing small RNA-seq reads for downstream quantification or discovery analysis.

原文语言：英语

small-rna-seq-target-prediction

Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally important miRNAs.

原文语言：英语

structural-biology-alphafold-predictions

Access and analyze AlphaFold protein structure predictions. Use when predicted structures are needed for proteins without experimental structures, or for confidence scores (pLDDT).

原文语言：英语

pdb-geometric-analysis

Perform geometric calculations on protein structures using Biopython Bio.PDB. Use when measuring distances, angles, and dihedrals, superimposing structures, calculating RMSD, or computing solvent accessible surface area (SASA).

原文语言：英语

structural-biology-modern-structure-prediction

Predict protein structures using modern ML models including AlphaFold3, ESMFold, Chai-1, and Boltz-1. Use when predicting structures for novel proteins, protein complexes, or when comparing predictions across multiple methods.

原文语言：英语

pdb-structure-io

Parse and write protein structure files using Biopython Bio.PDB. Use when reading PDB, mmCIF, and MMTF files, downloading structures from RCSB PDB, or writing structures to various formats.

原文语言：英语

pdb-structure-modification

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

原文语言：英语

pdb-structure-navigation

Navigate protein structure hierarchy using Biopython Bio.PDB SMCRA model. Use when accessing models, chains, residues, and atoms, iterating over structure levels, or extracting sequences from PDB files.

原文语言：英语

systems-biology-context-specific-models

Build tissue and condition-specific metabolic models using GIMME, iMAT, and INIT algorithms with expression data constraints. Create models that reflect cell-type specific metabolism. Use when building tissue-specific metabolic models or integrating…

原文语言：英语