Use when simulating RNA-seq or DNA-seq reads from a reference genome and GTF annotation file, optionally incorporating SNP variants and controlling expression profiles.

vimalinx0

Bioinformatics

Hmmscan

Use when searching protein sequences against profile hidden Markov models (HMMs) such as Pfam or other HMM databases.

vimalinx0

Bioinformatics

Pmc2bioc

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

vimalinx0

Bioinformatics

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.

vimalinx0

Bioinformatics

Rnaduplex

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

vimalinx0

Bioinformatics

Rpsblast

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

vimalinx0

Bioinformatics

Seqtk

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

vimalinx0

Bioinformatics

Starlong

Use when aligning long RNA-seq reads with STARlong through the CPU-dispatch wrapper installed in this environment.

vimalinx0

Bioinformatics

Sublong

Use when aligning long FASTQ reads to a reference genome with Subread's long-read aligner, optionally in RNA-seq mode.

vimalinx0

Bioinformatics

Tblastx

Use when searching nucleotide sequences against a nucleotide database using translated protein comparison. Useful for detecting distant evolutionary relationships between nucleotide sequences.

vimalinx0

Bioinformatics

Xa2multi Pl

Use when expanding BWA `XA:Z` alternate-alignment tags in SAM records into separate secondary SAM alignments for downstream tools.

vimalinx0

Bioinformatics

Vcf Query

Use when extracting and formatting specific fields from compressed VCF files, querying variants by region, or generating custom tabular output with genotype and INFO data.

vimalinx0

Bioinformatics

Use when parsing, extracting, or converting XML data from NCBI Entrez or other bioinformatics sources into tab-delimited tables. Use for selecting specific elements, filtering records, and restructuring hierarchical XML into flat formats for downstream analysis.

vimalinx0

Bioinformatics

SAELens: Sparse Autoencoders for Mechanistic Interpretability

Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.

John-Wang-08090

Bioinformatics

john-wang-0809-claw-research-skills-final-research-skills-link-downloads-by-theme-latest-02-literature-review-writing-citation-k-dense-ai-claude-scientific-skills-scientific-skills-scientific-schematics-skill-md

Create publication-quality scientific diagrams using Nano Banana Pro AI with smart iterative refinement. Uses Gemini 3 Pro for quality review. Only regenerates if quality is below threshold for your document type. Specialized in neural network architectures, system diagrams, flowcharts, biological pathways, and complex scientific visualizations.

John-Wang-08090

Bioinformatics Skills | Skills Pool

Bioinformatics

Bioinformatics

Fill Fs

Gbf2info

Gbf2facds

Hisat2 Simulate Reads Py

Hmmscan

Pmc2bioc

Psiblast

Rnaduplex

Rpsblast

Seqtk

Starlong

Sublong

Tblastx

Xa2multi Pl

Vcf Query

Xtract

SAELens: Sparse Autoencoders for Mechanistic Interpretability

john-wang-0809-claw-research-skills-final-research-skills-link-downloads-by-theme-latest-02-literature-review-writing-citation-k-dense-ai-claude-scientific-skills-scientific-skills-scientific-schematics-skill-md