All-in-one read preprocessing with fastp including adapter trimming, quality filtering, deduplication, base correction, and HTML report generation.
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard rea — from…
Filter reads by quality scores, length, and N content using Trimmomatic and fastp. Apply sliding window trimming, remove low-quality bases from read ends, and discard rea — from…
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresent — from…
Generate and interpret quality reports from FASTQ files using FastQC and MultiQC. Assess per-base quality, adapter content, GC bias, duplication levels, and overrepresent — from…
Generate consensus sequences and manage reference files using samtools. Use when creating consensus from alignments, indexing references, or creating sequence dictionarie — from…
Detect distant homologs using profile and structure-aware methods that go beyond standard BLAST. Use when sequence identity falls into the twilight zone (<35% pairwise), when…
Generates standardized quality control reports by aggregating metrics from FastQC, alignment, and other tools using MultiQC.
Exports publication-ready figures in various formats with proper resolution, sizing, and typography. Use when preparing figures for journal submission, creating vector gr — from…
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 dow — from…
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 dow — from…
Quality control and exploration of RNA-seq count matrices before differential expression. Check for outliers, batch effects, and sample relationships.
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.
Predicts RNA secondary structures using minimum free energy folding and partition function analysis with ViennaRNA (RNAfold, RNAalifold, RNAcofold).
View, convert, and understand SAM/BAM/CRAM alignment files using samtools and pysam. Use when inspecting alignments, converting between formats, or understanding alignmen — from…
Creates sashimi plots showing RNA-seq read coverage and splice junction counts using ggsashimi or rmats2sashimiplot.
Find homologous sequences using iterative BLAST (PSI-BLAST), profile HMMs (HMMER), and reciprocal best hit analysis.
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences.
Integrate multiple scRNA-seq samples/batches using Harmony, scVI, Seurat anchors, and fastMNN. Remove technical variation while preserving biological differences.
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
Automated cell type annotation using reference-based methods including CellTypist, scPred, SingleR, and Azimuth for consistent, reproducible cell labeling.
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis.
Infer cell-cell communication networks from scRNA-seq data using CellChat, NicheNet, and LIANA for ligand-receptor interaction analysis.
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectori — from…
Reconstruct cell lineage trees from CRISPR barcode tracing or mitochondrial mutations. Use when studying clonal dynamics, cell fate decisions, or developmental trajectori — from…
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types.
Analyze metabolite-mediated cell-cell communication using MeboCost for metabolic signaling inference between cell types.
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC — from…
Analyze multi-modal single-cell data (CITE-seq, Multiome, spatial). Use when working with data that measures multiple modalities per cell like RNA + protein or RNA + ATAC — from…
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.
Analyze Perturb-seq and CROP-seq CRISPR screening data integrated with scRNA-seq. Use when identifying gene function through pooled genetic perturbations in single cells.
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensionality reduction, clustering, peak calling, and moti — from…
Single-cell ATAC-seq analysis with Signac (R/Seurat) and ArchR. Process 10X Genomics scATAC data, perform QC, dimensionality reduction, clustering, peak calling, and moti — from…
Analyzes alternative splicing at single-cell resolution using BRIE2 for probabilistic PSI estimation or leafcutter2 for cluster-based analysis with NMD detection.
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis.
Infer developmental trajectories and pseudotime from single-cell RNA-seq data using Monocle3, Slingshot, and scVelo for RNA velocity analysis.
Perform differential expression analysis of miRNAs between conditions using DESeq2 or edgeR with small RNA-specific considerations.
Discover novel miRNAs and quantify known miRNAs using miRDeep2 de novo prediction from small RNA-seq data.
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 e — from…
Preprocess small RNA sequencing data with adapter trimming and size selection optimized for miRNA, piRNA, and other small RNAs.
Predict miRNA target genes using sequence-based algorithms and database lookups. Use when identifying potential mRNA targets of differentially expressed or functionally i — from…
Comprehensive guide to bio specialized 16. Master the concepts, implementation, best practices, and real-world applications of bio specialized 16 in professional environments.
Master bio specialized skill 105 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 181 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 25 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 275 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 37 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 86 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Master bio specialized skill 98 with comprehensive coverage of concepts, implementation, optimization, and production best practices.
Predicts whether a DNA variant alters mRNA splicing using sequence-based deep-learning tools — SpliceAI (10kb context dilated CNN, clinical default), Pangolin (multi-tissue),…
End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq.
Assesses RNA-seq data quality for splicing analysis including junction saturation curves, splice site strength scoring, and junction coverage metrics using RSeQC.
Quantifies alternative splicing as PSI (percent spliced in) from RNA-seq using rMATS-turbo (BAM-based event), SUPPA2 (TPM-based event), MAJIQ V3 (LSV-based Bayesian), leafcutter…
Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror.
Aggregate results, train ML models, and produce reports with validated references.
A conversational framework for systematic scientific problem selection, project ideation, troubleshooting, and strategic decision making.
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework.
Analyze BCR repertoires for somatic hypermutation, clonal lineages, and B cell phylogenetics using the Immcantation framework.
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes — from…
Perform V(D)J alignment and clonotype assembly from TCR-seq or BCR-seq data using MiXCR. Use when processing raw immune repertoire sequencing data to identify clonotypes — from…