3,259 件 ・ 関連度順
概要と使いどころ
Calls DNA methylation from Oxford Nanopore sequencing data using signal-level analysis. Use when detecting 5mC or 6mA modifications directly from nanopore reads without bisulfite conversion.
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Analyzes cfDNA methylation patterns for cancer detection using cfMeDIP-seq or bisulfite sequencing with MethylDackel. Identifies cancer-specific methylation signatures and performs tissue-of-origin deconvolution. Use when using methylation biomarkers for early cancer detection or minimal residual disease.
日本語の概要は準備中です。原文の説明を表示しています。
Detect antimicrobial resistance genes using AMRFinderPlus, ResFinder, and CARD. Screen isolates and metagenomes for resistance determinants. Use when characterizing resistance profiles in clinical isolates, surveillance samples, or metagenomic data.
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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.
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Balance, normalize, and transform Hi-C contact matrices using cooler and cooltools. Apply iterative correction (ICE), compute expected values, and generate observed/expected matrices. Use when normalizing or transforming Hi-C matrices.
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Predict B-cell and T-cell epitopes using BepiPred, IEDB tools, and structure-based methods for vaccine and antibody design. Identify immunogenic regions in antigens. Use when designing vaccines, mapping antibody binding sites, or predicting immunogenic peptides.
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Profile functional potential of metagenomes using HUMAnN3 and similar tools. Use when obtaining pathway abundances, gene family counts, or functional annotations from metagenomic data.
日本語の概要は準備中です。原文の説明を表示しています。
Extract methylation calls from Bismark BAM files using bismark_methylation_extractor. Generates per-cytosine reports for CpG, CHG, and CHH contexts. Use when extracting methylation levels from aligned bisulfite sequencing data for downstream analysis.
日本語の概要は準備中です。原文の説明を表示しています。
Differentially methylated region (DMR) detection using methylKit tiles, bsseq BSmooth, and DMRcate. Use when identifying contiguous genomic regions with methylation differences between experimental conditions or cell types.
日本語の概要は準備中です。原文の説明を表示しています。
Compare Hi-C contact matrices between conditions to identify differential chromatin interactions. Compute log2 fold changes, statistical significance, and visualize differential contact maps. Use when comparing Hi-C contacts between conditions.
日本語の概要は準備中です。原文の説明を表示しています。
Load and preprocess imaging mass cytometry (IMC) and MIBI data. Covers MCD/TIFF handling, hot pixel removal, and image normalization. Use when starting IMC analysis from raw MCD files or preparing images for segmentation.
日本語の概要は準備中です。原文の説明を表示しています。
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 calling, SV detection, or coverage analysis.
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Quality control and normalization for metabolomics data. Covers QC-based correction, batch effect removal, and data transformation methods. Use when correcting technical variation in metabolomics data before statistical analysis.
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Map metabolites to biological pathways using KEGG, Reactome, and MetaboAnalyst. Perform pathway enrichment and topology analysis. Use when interpreting metabolomics results in the context of biochemical pathways.
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Targeted metabolomics analysis using MRM/SRM with standard curves. Covers absolute quantification, method validation, and quality assessment. Use when quantifying specific metabolites using calibration curves and internal standards.
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Predict peptide-MHC class I and II binding affinity using MHCflurry and NetMHCpan neural network models. Identify potential T-cell epitopes from protein sequences. Use when predicting MHC binding for vaccine design or neoantigen identification.
日本語の概要は準備中です。原文の説明を表示しています。
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 working within QIIME2 ecosystem.
日本語の概要は準備中です。原文の説明を表示しています。
Bisulfite sequencing read alignment using Bismark with bowtie2/hisat2. Handles genome preparation and produces BAM files with methylation information. Use when aligning WGBS, RRBS, or other bisulfite-converted sequencing reads to a reference genome.
日本語の概要は準備中です。原文の説明を表示しています。
XCMS3 workflow for LC-MS/MS metabolomics preprocessing. Covers peak detection, retention time alignment, correspondence (grouping), and gap filling. Use when processing raw LC-MS data into a feature table for untargeted metabolomics.
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Tracks ctDNA dynamics over time for treatment response monitoring using serial liquid biopsy samples. Analyzes tumor fraction trends, mutation clearance kinetics, and defines molecular response criteria. Use when monitoring patients during therapy or detecting molecular relapse before clinical progression.
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Marker gene-based taxonomic profiling using MetaPhlAn 4. Provides accurate species-level relative abundances using clade-specific markers. Use when accurate taxonomic profiling is needed and computational resources are limited, or for comparison with HMP/other MetaPhlAn studies.
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Score and prioritize neoantigens and epitopes for immunogenicity using multi-factor models combining MHC binding, processing, expression, and sequence features. Rank candidates for vaccine design. Use when prioritizing epitopes for vaccine development or identifying the most immunogenic neoantigens.
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Metabolite identification from m/z and retention time. Covers database matching, MS/MS spectral matching, and confidence level assignment. Use when assigning compound identities to detected features in untargeted metabolomics.
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Detect structural variants from long-read alignments using Sniffles, cuteSV, and SVIM. Use when detecting deletions, insertions, inversions, translocations, or complex rearrangements from ONT or PacBio data, especially those missed by short-read methods.
日本語の概要は準備中です。原文の説明を表示しています。