「sequencing」の検索結果

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. SpliceWiz is a user-friendly and performance-optimized R package for AS analysis, by processing alignment BAM files to quantify read counts across splice junctions, IRFinder-based intron retention quantitation, and supports novel splicing event identification. We introduce a novel visualization for AS using normalized coverage, thereby allowing visualization of differential AS across

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Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.

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Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

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Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression

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BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of unknown cell types. BUSseq is able to simultaneously correct batch effects, clusters cell types, and takes care of the count data nature, the overdispersion, the dropout events, and the cell-specific sequencing depth of scRNA-seq data. After correcting the batch effects with BUSseq, the corrected value ca

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The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, an

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PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. Buliding upon the RangedSummarizedExperiment class, PhIPData enables users to coordinate metadata with experimental data in analyses. Additionally, PhIPData provides specialized methods to subset and identify beads-only samples, subset objects using virus aliases, and use existing peptide libraries to populate object parameters.

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A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. The package implements methods to fit regression mixture models for a probabilistic classification of cells, including multiplet detection. Demultiplexing error rates can be estimated, and methods for quality control are provided.

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When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups. FindIndel() and IndelForm() function will help you align each read to reference sequence and generate scar form strings respectively. IndelIdents() function will help you to define a scar form for each cell or read. IndelPlot() function will help you to visualize the distribution of deletion and insertion. TagPro

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Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. This package calls and reports cytosine methylation as well as frequencies of hypermethylated epialleles at the level of genomic regions or individual cytosines in next-generation sequencing data using binary alignment map (BAM) files as an input. Among other things, this package can also extract and visualise methylation patterns and assess allele specificity of methylation.

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The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose

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BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. Given a PhIPData object, BEER returns posterior probabilities of enriched antibody responses, point estimates for the relative fold-change in comparison to negative control samples, and more. Additionally, BEER provides a convenient implementation for using edgeR to identify enriched antibody responses.

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Designs a deliberate sequence of offers (attraction, upsell, downsell, continuity) so a new customer generates enough cash within ~30 days to fund acquiring the next one - Alex Hormozi's client-financed acquisition. Use when customers buy once and never again, when CAC eats all the profit, when you can't afford to advertise profitably, when the business grows but cash shrinks, when you sell one product at one price, when deciding what to sell first or next, or when structuring upsells, downsells, payment plans, trials, and continuity. Covers the 30-day payback rule, attraction/upsell/downsell/continuity offer types, and cash-flow sequencing for validated markets.

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Run nf-core bioinformatics pipelines (rnaseq, sarek, atacseq) on sequencing data. Use when analyzing RNA-seq, WGS/WES, or ATAC-seq data—either local FASTQs or public datasets from GEO/SRA. Triggers on nf-core, Nextflow, FASTQ analysis, variant calling, gene expression, differential expression, GEO reanalysis, GSE/GSM/SRR accessions, or samplesheet creation.

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Use when a database schema or data-meaning change needs Parallel Change, including expand, migrate, and contract sequencing for column renames, type or data reinterpretation, large-table backfills, relationship-table changes, enum/status transitions, timezone/default changes, and index or uniqueness changes. This should trigger before framework-specific Flyway implementation guidance when deciding whether a migration needs a compatibility window or whether a simpler migration is sufficient. Part of Plinth Toolkit

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Use when managing multiple initiatives across time horizons (now/next/later, H1/H2/H3), balancing risk vs return across portfolio, sizing and sequencing bets with dependencies, setting exit/scale criteria for experiments, allocating resources across innovation types (core/adjacent/transformational), or when user mentions portfolio planning, roadmap horizons, betting framework, initiative prioritization, innovation portfolio, or resource allocation across horizons.

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Optimize prefabrication and modular construction workflows. Plan module sequencing, factory scheduling, transportation logistics, and on-site assembly for maximum efficiency.

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Run a go-to-market war room for a launch, repositioning, price change, or new product. Convenes opposing expert and customer-persona viewpoints to debate the plan, surfaces the risks that kill launches, and returns a go/no-go call plus a phased rollout plan with owners, sequencing, and kill criteria. Use before any launch you can't easily walk back.

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Designs the contract for an API change inside one codebase — a component's props, a function surface, URL or query parameters, an event payload, or a module boundary — through a discovery pass, an options document with one recommendation, a question round, and an adversarial validation round, with every element of the contract justified from one stated goal. Use when you want to design, shape, decide, or nail down an interface, contract, signature, or API change for a capability you can already describe, sized for roughly one pull request. Produces a design document and changes no code. Does not specify what a feature should do — use plan-a-feature. Does not plan delivery or sequencing — use plan-implementation. Does not assess the architecture of existing code — use architectural-analysis. Does not write the code — use tdd. Does not restructure existing code — use refactor. Runs its rounds without pausing for review; to review each round as it lands, use pairing.

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The order of operations for an Active Directory penetration test: setup, collection, exploitation, post-processing. Use this whenever you are planning or driving an AD assessment and need to know what to run before what and why (map before you exploit; harvest easy credentials before spraying to avoid lockouts; collect the graph before you reason about paths). Covers phase sequencing with standard tooling: netexec/nxc, impacket, certipy, bloodyAD, kerbrute, BloodHound CE. Invoke it at the start of an engagement, when deciding the next phase, or when a step feels out of order.

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Think and work like an expert Glycobiologist. Use when a task calls for Glycobiologist judgment. Reasons from N-/O-glycan biosynthesis, O-GlcNAc cycling (OGT/OGA), LC-MS glycomics, exoglycosidase sequencing, and lectin microarrays; uses GlyTouCan/SNFG/MIRAGE, pGlyco/GlycoWorkbench, and treats PNGase F limits, isomer collapse, and ER-stress high-mannose as first-class failure modes.

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Think and work like an expert Genomicist. Use when a task calls for Genomicist judgment. Reasons from reference-relative coordinates, haplotypes, variant classes, and sequencing-as-measurement through GATK/DeepVariant, VEP/ClinVar/gnomAD, GIAB/hap.py benchmarking, and ACMG/AMP-ClinGen frameworks while treating build mismatches, paralog/pseudogene and GC dropout artifacts, contamination and index hopping, batch effects, and annotation drift as first-class failure modes.

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Resolve the architecture of focal oncogene amplifications — extrachromosomal DNA (ecDNA), breakage-fusion-bridge (BFB) cycles, homogeneously staining regions (HSR), and linear amplification — from whole-genome sequencing with AmpliconArchitect, the AmpliconSuite pipeline, and AmpliconClassifier. Covers copy-number seed selection, breakpoint-graph reconstruction, balanced-flow optimization, ecDNA classification, and the limits of depth-only amplification calls. Use when a focal amplification needs structural characterization, when distinguishing ecDNA from chromosomal amplification, suspecting ecDNA-driven oncogene amplification or therapy resistance, or selecting copy-number seeds for amplicon reconstruction.

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Quantifies CRISPR editing outcomes with CRISPResso2 (Clement 2019 Nat Biotechnol) across Cas9-nuclease (indels, HDR), CBE and ABE base editors (target conversion + bystander), and prime editor (pegRNA-templated) modes. Covers single-amplicon (CRISPResso), multi-sample batch (CRISPRessoBatch), pooled-amplicon (CRISPRessoPooled), WGS off-target (CRISPRessoWGS), and sample-comparison (CRISPRessoCompare) workflows; quantification-window math that controls what is called edited; substitution-vs-indel diagnostic to distinguish BE from Cas9 contamination; MMEJ deletion pattern interpretation; allele-frequency tables; and failure modes from amplicon misalignment or contamination. Use when quantifying editing from amplicon sequencing, choosing CRISPResso mode by design, distinguishing intended edits from bystanders and indel byproducts, debugging low-alignment runs, or generating publication-grade editing reports.

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