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Orchestrates an end-to-end MeRIP-seq / m6A-seq analysis from raw FASTQ to differential m6A peak calls and metagene plots, chaining fastp adapter trimming, STAR splice-aware genome alignment (NO deduplication for non-UMI MeRIP), deepTools replicate-concordance + IP-enrichment QC, PreSeq saturation...
Assesses RNA-seq data quality specifically for alternative splicing analysis. QC layers include experimental design audit (library prep, read length, depth, replicates), STAR 2-pass cohort-style alignment, junction saturation curves and discovery plateau detection, novel-vs-known junction ratio d...
End-to-end bulk RNA-seq orchestrator — takes raw FASTQ reads through QC and trimming (FastQC, fastp/Trim Galore), alignment and quantification (STAR, Salmon, featureCounts), assembles a gene-level counts matrix, then hands off to differential expression (pydeseq2), pathway/GSEA enrichment (pathwa...
End-to-end alternative splicing analysis from FASTQ to differential splicing results. Aligns with STAR 2-pass mode, performs junction QC, runs rMATS-turbo for differential analysis, and generates sashimi visualizations. Use when performing comprehensive splicing analysis from raw RNA-seq data.
Align and QC MeRIP-seq IP and input samples for m6A analysis. Use when preparing MeRIP-seq data for peak calling or differential methylation analysis.
STAR alignment skill for splice-aware RNA-seq read mapping with comprehensive QC metrics
End-to-end CLIP-seq pipeline from FASTQ to ENCODE-compliant binding sites, single-nucleotide crosslink maps, annotation, motifs, and (optionally) differential binding. Use when running the full Yeo lab eCLIP / iCLIP / iCLIP2 / iCLIP3 / irCLIP / PAR-CLIP analysis with SMInput control, protocol-spe...
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. Use when running RNA-seq from FASTQ to DE results.
End-to-end alternative splicing analysis from FASTQ to differential splicing results for short-read bulk RNA-seq. Aligns with STAR 2-pass cohort-style, performs junction QC (RSeQC, MaxEntScan, SpliceAI), runs rMATS-turbo and leafcutter for concordant differential analysis, optionally MAJIQ V3 for...
Align preprocessed CLIP-seq reads (eCLIP, iCLIP, iCLIP2, PAR-CLIP) to genome with STAR or bowtie2 using crosslink-preserving parameters, choosing between unique-mapper-only and multi-mapper-aware alignment for repeat-binding RBPs, deciding STAR vs HISAT2 memory trade-offs, and applying ENCODE-com...
Aligns and QCs methylated-RNA-immunoprecipitation (MeRIP / m6A-seq) IP and input libraries using STAR or HISAT2 splice-aware mapping, samtools sort/index, IP/input matched-pair tracking, antibody-lot metadata recording, replicate concordance via deepTools multiBamSummary + plotCorrelation, IP enr...
Agent skill for Data Scientist, ML / AI Engineer, Researcher, published by BioTender-max. Project details and file access are provided by the publisher.
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