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Skills في هذا المستودع
جمع SkillsMP عدد ٥٦٢ من skills من GPTomics/bioSkills. افتح أي skill لمراجعة مصدره وتفاصيله.
GPTomics/bioSkillsعرض ٤٠ من أصل ٥٦٢ skills مجمعة.
Reconstructs single-cell lineage trees and clonal relationships from CRISPR/Cas9 scars, static expressed barcodes (LARRY/CellTag), or somatic mtDNA mutations using Cassiopeia, Startle, and CoSpar. Use when building a phylogeny from barcode scars, choosing a…
لغة النص الأصلي: الإنجليزية
Detect cluster marker genes and assign manual cell type labels in single-cell RNA-seq using Scanpy (Python) and Seurat (R). Use when finding genes that distinguish clusters, ranking markers for annotation, scoring gene signatures, hand-labeling clusters, or…
لغة النص الأصلي: الإنجليزية
Infers metabolite-mediated cell-cell communication from scRNA-seq by scoring enzyme-to-sensor pairs (MEBOCOST), with metabolic flux (scFEA), FBA state (Compass), and neurotransmitter (NeuronChat) alternatives. Use when studying metabolic crosstalk between…
لغة النص الأصلي: الإنجليزية
Integrate multimodal single-cell data (CITE-seq RNA+protein, 10x Multiome RNA+ATAC, unpaired/diagonal RNA+ATAC) and choose the right joint method. Use when classifying an integration task by anchor structure (paired vs unpaired), denoising CITE-seq ADT…
لغة النص الأصلي: الإنجليزية
Analyze Perturb-seq / CROP-seq single-cell CRISPR screens. Use when assigning guides as a mixture problem, removing non-perturbed escaper cells with Mixscape, choosing a calibrated test (SCEPTRE conditional resampling) over naive DE, quantifying effect size…
لغة النص الأصلي: الإنجليزية
Quality control, ambient-RNA handling, normalization, and feature selection for single-cell RNA-seq using Scanpy (Python) and Seurat (R). Use when filtering low-quality cells with MAD-adaptive thresholds, setting tissue-aware mito cutoffs, removing ambient…
لغة النص الأصلي: الإنجليزية
Analyze single-cell ATAC-seq with Signac/ArchR (R) and SnapATAC2 (Python alternative). Use when processing scATAC fragments, choosing a framework, calling consensus peaks, running TF-IDF/LSI while diagnosing the depth component, scoring chromVAR motif…
لغة النص الأصلي: الإنجليزية
Infers developmental trajectories, pseudotime, RNA velocity, and directed fate probabilities from single-cell data using PAGA, Slingshot, Monocle3, DPT, Palantir, scVelo, and CellRank 2. Use when ordering cells along a differentiation continuum, choosing a…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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.
لغة النص الأصلي: الإنجليزية
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.
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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,…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية
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…
لغة النص الأصلي: الإنجليزية