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Differential abundance testing for microbiome data using compositionally-aware methods like ALDEx2, ANCOM-BC2, and MaAsLin2. Use when identifying taxa that differ between experimental groups while accounting for the compositional nature of microbiome data.
Agent skill for Data Scientist, Business Intelligence Analyst, Researcher, published by BioTender-max. Project details and file access are provided by the publisher.
Agent skill for Researcher, Data Scientist, ML / AI Engineer, published by BioTender-max. Project details and file access are provided by the publisher.
Agent skill for Data Analyst, ML / AI Engineer, Researcher, published by FridrichMethod. Project details and file access are provided by the publisher.
Agent skill for Data Analyst, ML / AI Engineer, Researcher, published by Rudson-Oliveira. Project details and file access are provided by the publisher.
Agent skill for Data Analyst, Business Intelligence Analyst, Researcher, published by GPTomics. Project details and file access are provided by the publisher.
Agent skill for Data Analyst, Data Scientist, ML / AI Engineer, published by BioTender-max. Project details and file access are provided by the publisher.
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...
Identify differentially accessible chromatin regions across conditions using DiffBind, csaw, DESeq2, or edgeR. Use when comparing ATAC-seq accessibility between treatment groups, choosing between consensus-peak vs sliding-window approaches, picking the correct normalization (full library vs reads...
Batch effect correction for CRISPR screens covering ComBat empirical-Bayes, RUV, SVA, control-sgRNA normalization, and the model-based alternative of including batch as a covariate in MAGeCK MLE or Chronos. Covers screen-specific batch sources (passage cohort, library lot, infection day, sequenci...
Creates DE-specific diagnostic and result visualizations using DESeq2/edgeR built-in functions and lightweight ggplot2 wrappers. Covers MA plot (with the shrunken-LFC compression effect), volcano (with the apeglm caveat that p-values are unchanged), PCA on VST/rlog (never raw counts), sample dist...
Estimates the minimum biological replicates (or cells/events) for a target power at a target FDR in genomics experiments using ssizeRNA, PROPER, powsimR for scRNA-seq, and pilot-data dispersion estimation from DESeq2/edgeR. Covers the biological-versus-technical replication distinction (technical...
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