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SkillsMP 已收集 PKU-YuanGroup/OpenAI4S 中的 604 个 Skill。打开任一 Skill 可查看来源和详情。
PKU-YuanGroup/OpenAI4S已展示 40 / 604 个已收集 Skill。
Aggregates per-tool QC metrics (FastQC, fastp, alignment, quantification, variant calling, single-cell) into one interactive MultiQC report, and guides module scoping, sample-name resolution, large-cohort behavior, and turning the report into an actual QC…
原文语言：英语
Exports publication-ready figures with the correct vector/raster split, embedded editable fonts, color-space-robust palettes, and journal-correct sizing and resolution in matplotlib and ggplot2. Use when preparing figures for journal submission, exporting a…
原文语言：英语
Runs parameterized Jupyter notebooks as reproducible batch report generators with papermill, renders them to HTML/PDF with nbconvert, aggregates results across samples, and makes notebook outputs trustworthy. Use when generating per-sample analysis reports,…
原文语言：英语
Builds publication-ready tables - descriptive Table 1, regression and differential-expression result tables, and supplementary tables - with gtsummary, gt, flextable, and kableExtra (R) or great_tables, pandas, and tableone (Python), choosing the right…
原文语言：英语
Builds reproducible Quarto reports, presentations, and websites across R, Python, and Julia, with correct engine selection, cache-vs-freeze semantics, native cross-references, parameters, and environment pinning. Use when creating a Quarto report of an…
原文语言：英语
Creates reproducible R Markdown analysis reports (HTML, PDF, Word) with knitr, covering the render pipeline, the interactive-vs-knit session trap, cache invalidation, bookdown cross-references, parameterization, and environment pinning. Use when generating an…
原文语言：英语
Select restriction enzymes for cloning or diagnostics using Biopython Bio.Restriction. Finds enzymes by cut frequency, overhang type, recognition-site length, commercial availability, compatible ends, and methylation sensitivity, and identifies isoschizomers…
原文语言：英语
Predict restriction digest fragment sizes and gel patterns using Biopython Bio.Restriction. Computes fragment lengths and sequences for single and double digests on linear or circular DNA, and interprets them against an agarose gel. Use when predicting the…
原文语言：英语
Design and validate Type IIS scarless DNA assembly (Golden Gate, MoClo) using Biopython Bio.Restriction. Screens parts for internal BsaI/BsmBI/BbsI/SapI sites (domestication), previews the fusion overhangs a digest exposes, and validates a fusion-overhang set…
原文语言：英语
Build restriction maps showing enzyme cut positions and inter-site distances along DNA using Biopython Bio.Restriction. Produces text or graphical maps for linear and circular molecules, orders sites from single and double digests, and overlays GenBank…
原文语言：英语
Find restriction enzyme cut sites in DNA sequences using Biopython Bio.Restriction. Searches single enzymes, batches, or commercial enzyme sets and returns cut positions for linear or circular DNA. Use when locating where one or more restriction enzymes cut a…
原文语言：英语
Map translation initiation sites, including non-AUG and alternative starts, from initiation-drug ribosome profiling (TI-seq). Use when locating start codons, detecting near-cognate or upstream initiation, or analyzing harringtonine, lactimidomycin…
原文语言：英语
Detect and quantify translated ORFs from Ribo-seq using 3-nucleotide periodicity, including uORFs, internal ORFs, dORFs, and novel ORFs. Use when finding actively translated regions beyond annotated CDS, classifying ORFs by the 2022 community standard,…
原文语言：英语
Preprocess ribosome profiling reads with UMI handling, adapter trimming, contaminant/rRNA depletion, and footprint-aware alignment. Use when preparing Ribo-seq FASTQ for periodicity QC, ORF detection, translation efficiency, or stalling analysis, or when…
原文语言：英语
Validate Ribo-seq library quality by measuring 3-nucleotide periodicity and calibrating read-length-specific P-site offsets. Use when checking whether footprints capture genuine translation, determining P-site offsets for downstream ORF/TE/stalling analysis,…
原文语言：英语
Detect ribosome pausing and stalling at codon resolution from Ribo-seq, using local-relative occupancy metrics and A-site assignment. Use when studying elongation dynamics, codon dwell times, pause motifs, or ribosome collisions, and when judging whether a…
原文语言：英语
Quantify translation efficiency (TE) as ribosome occupancy relative to mRNA abundance and test for differential TE between conditions. Use when separating translational from transcriptional regulation, distinguishing genuine translational control from…
原文语言：英语
Quantify transcript expression from FASTQ with Salmon (selective alignment) or kallisto (pseudoalignment), bypassing genome mapping. Use when quantifying RNA-seq without alignment, deciding whether a decoy-aware index is required, detecting and verifying…
原文语言：英语
Quality control and exploration of RNA-seq count matrices before differential expression. Use when checking library sizes and composition, choosing VST vs rlog for visualization, running PCA and sample correlation, detecting outliers with Cook's distance,…
原文语言：英语
Count reads per gene from aligned BAM files using Subread featureCounts. Use when turning STAR/HISAT2 BAMs into a gene-level count matrix for DESeq2/edgeR, deciding library strandedness, handling paired-end fragment counting, choosing how to treat…
原文语言：英语
Import transcript-level quantifications from Salmon/kallisto/RSEM into R for gene-level analysis with DESeq2/edgeR using tximport or tximeta. Use when summarizing transcript abundances to gene counts with the correct length offset, choosing a…
原文语言：英语
Tests whether a proposed or predicted RNA secondary structure is supported by evolutionary covariation using R-scape, which scores compensatory substitutions against a phylogeny-aware null and estimates the statistical power of the alignment. Use when…
原文语言：英语
Searches for non-coding RNA homologs and classifies RNA families with Infernal covariance models against Rfam, scoring sequence AND secondary-structure conservation jointly. Use when deciding whether a covariance model is the right tool versus BLAST/nhmmer…
原文语言：英语
Predicts RNA secondary structure with ViennaRNA, treating the Boltzmann ensemble (partition function, base-pair probabilities, centroid, MEA, stochastic samples) as the object rather than a single MFE fold. Covers consensus folding from alignments…
原文语言：英语
Processes experimental RNA structure probing data (SHAPE-MaP, DMS-MaPseq) into per-nucleotide reactivity profiles with ShapeMapper2, then uses them as soft restraints on thermodynamic folding. Covers reagent and readout choice (SHAPE vs DMS,…
原文语言：英语
Process many sequence files in batch (count, merge, split, convert, summarize) with memory-safe streaming and on-disk indexing using Biopython, pysam, or pyfastx. Use when iterating over a directory of FASTA/FASTQ files, merging or splitting datasets,…
原文语言：英语
Read, write, and index compressed sequence files (gzip, bzip2, xz, BGZF) with Biopython and bgzip/samtools. Use when working with .gz, .bz2, or .bgz sequence files, when random access into a compressed FASTA/FASTQ is needed, or when SeqIO.index/faidx/tabix…
原文语言：英语
Work with FASTQ quality scores using Biopython - access Phred scores, filter and trim by quality, compute per-position profiles, and convert between Sanger/Phred+33, Solexa, and Illumina/Phred+64 encodings. Use when analyzing read quality, filtering or…
原文语言：英语
Filter and select sequences by criteria (length, ID, GC content, N content, motifs, patterns, description) using Biopython, streaming so large files never load into RAM. Use when subsetting a FASTA/FASTQ file, removing unwanted or low-quality records, or…
原文语言：英语
Convert between sequence file formats (FASTA, FASTQ, GenBank, EMBL, Stockholm) and re-encode FASTQ quality offsets using Biopython Bio.SeqIO. Use when changing a file format for a downstream tool, fixing FASTQ quality encoding (Phred+33 vs Phred+64 vs…
原文语言：英语
Handle paired-end FASTQ files (R1/R2) using Biopython while keeping mates synchronized. Use when working with Illumina paired reads, synchronizing pairs, filtering both mates together with orphan routing, interleaving/deinterleaving, or matching mates by read…
原文语言：英语
Read biological sequence files (FASTA, FASTQ, GenBank, EMBL, ABI, SFF) with Biopython Bio.SeqIO, choosing between streaming, in-memory, and on-disk-indexed access. Use when parsing sequence files, iterating multi-record files, randomly accessing records by ID…
原文语言：英语
Calculate assembly and sequence statistics (N50/L50, auN, NG50/NGA50, length distribution, GC content with ambiguity handling, summary reports) using Biopython. Use when analyzing sequence datasets, generating QC reports, or comparing genome assemblies.
原文语言：英语
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
Analyze codon usage and calculate CAI (Codon Adaptation Index), RSCU, and Nc with Biopython, and produce naive max-CAI codon-optimized sequences. Use when scoring a gene's codon bias against a host, optimizing a CDS for heterologous expression, or studying…
原文语言：英语
Find sequence motifs, degenerate IUPAC patterns, and transcription-factor binding sites in DNA/RNA using Biopython and regex, including position weight matrix (PWM/PSSM) scoring. Use when locating regulatory elements, counting overlapping motif occurrences,…
原文语言：英语
Generate reverse complements and complements of DNA/RNA sequences using Biopython, including IUPAC ambiguity codes, gapped alignments, and minus-strand features. Use when working with the opposite strand, building reverse primers, normalizing strand…
原文语言：英语
Create and manipulate Seq, MutableSeq, and SeqRecord objects using Biopython. Use when creating sequences from strings, modifying sequence data in-place, building annotated records for file output, or debugging post-1.78 Bio.Alphabet and immutability errors.
原文语言：英语
Calculate nucleotide and protein sequence properties (GC content, GC skew, molecular weight, melting temperature, isoelectric point, instability, hydropathy) with Biopython. Use when analyzing sequence composition, computing primer Tm, estimating DNA or…
原文语言：英语
Slice, extract, and concatenate biological sequences and annotated records using Biopython. Use when extracting subsequences by position, splicing exons into a transcript, joining sequences, or carrying a sub-region of an annotated record (with quality scores…
原文语言：英语