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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 a...
Load spatial transcriptomics data from Visium, Xenium, MERFISH, Slide-seq, and other platforms using Squidpy and SpatialData. Read Space Ranger outputs, convert formats, and access spatial coordinates.
Convert raw Nanopore signal data (FAST5/POD5) to nucleotide sequences using Dorado or Guppy basecallers. Covers model selection, GPU acceleration, modified base detection, and quality filtering. Use when proces...
Call topologically associating domains (TADs) from Hi-C data using insulation score, HiCExplorer, and other methods. Identify domain boundaries and hierarchical domain structure.
Create reproducible bioinformatics analysis reports with R Markdown including code, results, and visualizations in HTML, PDF, or Word format.
Find cross-references between NCBI databases using Biopython Bio.Entrez. Use for navigating from genes to proteins, sequences to publications, finding related records, and discovering database relationships.
Retrieve records from NCBI databases using Biopython Bio.Entrez. Use for downloading sequences, fetching GenBank records, getting document summaries, and parsing NCBI data into Biopython objects.
Search NCBI databases using Biopython Bio.Entrez. Use for finding records by keyword, building search queries, discovering database structure, and getting global query counts across databases.
Access and analyze AlphaFold protein structure predictions. Use when you need predicted structures for proteins without experimental structures, or confidence scores (pLDDT).
DNA methylation analysis with methylKit in R. Import Bismark coverage files, filter by coverage, normalize samples, and perform statistical comparisons. Use when analyzing single-base methylation patterns, comp...
End-to-end RNA-seq workflow from FASTQ files to differential expression results. Covers QC, quantification (Salmon or STAR+featureCounts), and DESeq2 analysis with visualization.
Reactome pathway enrichment using ReactomePA package. Performs over-representation analysis and GSEA on Reactome pathways, a curated peer-reviewed knowledgebase of biological pathways. Supports visualization an...
Find differentially accessible chromatin regions between conditions using DiffBind or DESeq2. Use when comparing chromatin accessibility between treatment groups, cell types, or developmental stages in ATAC-seq...
Statistical testing for differentially abundant proteins between conditions. Covers limma and MSstats workflows with multiple testing correction. Use when identifying proteins with significant abundance changes...
Query NCBI Gene Expression Omnibus (GEO) for expression datasets using Biopython Bio.Entrez. Use for finding microarray/RNA-seq datasets, downloading expression data, and linking GEO to SRA.
Annotate ChIP-seq peaks to genomic features and genes using ChIPseeker. Assign peaks to promoters, exons, introns, and intergenic regions. Find nearest genes and calculate distance to TSS. Generate annotation p...
Align long reads using minimap2 for Oxford Nanopore and PacBio data. Supports various presets for different read types and applications. Use when aligning ONT or PacBio reads to a reference genome for variant c...
QIIME2 command-line workflow for 16S/ITS amplicon analysis. Alternative to DADA2/phyloseq R workflow with built-in provenance tracking. Use when preferring CLI over R, needing reproducible provenance, or workin...
Process Hi-C read pairs using pairtools. Parse alignments, filter duplicates, classify pairs, and generate contact statistics from Hi-C sequencing data.
Download sequencing data from NCBI SRA using the SRA toolkit. Use for downloading FASTQ files from SRA accessions, prefetching large datasets, validating downloads, and configuring SRA toolkit.
Design qPCR primers and TaqMan/molecular beacon probes using primer3-py. Configure probe Tm, primer-probe spacing, and hydrolysis probe constraints for real-time PCR assays.
End-to-end genome assembly workflow from reads to polished assembly with QC. Supports short reads (SPAdes), long reads (Flye), and hybrid approaches.
Download large datasets from NCBI efficiently using history server, batching, and rate limiting. Use for bulk sequence downloads, large query results, and production-scale data retrieval.
Predict metagenome functional content from 16S rRNA marker gene data using PICRUSt2. Infer KEGG, MetaCyc, and EC abundances from ASV tables. Use when functional profiling is needed from 16S data without shotgun...
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