「remove」の検索結果

Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across 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。

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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。

Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.

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。

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, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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。

Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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。

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias 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。

Strip designs to their essence by removing unnecessary complexity. Great design is simple, powerful, and clean. Use when the user asks to simplify, declutter, reduce noise, remove elements, or make a UI cleaner and more focused.

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。

Audit and rewrite content to remove 21 categories of AI writing patterns with a 43-entry replacement table

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。

Conversion-focused design that removes friction and guides users toward action through clarity, trust, and speed.

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。

Implement GNOME's 4-tier destructive-action pattern: undo toasts instead of confirmation dialogs, AdwAlertDialog for irreversible actions. Use when adding delete, remove, clear, or other destructive actions.

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。

Clear the freeze boundary set by /freeze, allowing edits to all directories again. Use when you want to widen edit scope without ending the session. Use when asked to "unfreeze", "unlock edits", "remove freeze", or "allow all edits". (gstack)

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。

Execute AEM Edge Delivery Services admin operations - list admins, add/remove users, preview, publish, unpublish content, clear cache, sync code, reindex, generate sitemap, manage snapshots, view logs, manage jobs, list sites, configure org/site settings, manage secrets and API keys. Also supports Document Authoring (DA) operations via admin.da.live - list/get/put content, copy, move, delete, versioning, and DA-specific preview/publish. Use for any Edge Delivery Services administrative task.

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 two versions of an AEM Edge Delivery Services page to identify what changed. Fetches preview vs live, or two different URLs, and produces a detailed content diff showing added, removed, and modified content, metadata, and blocks. Use when reviewing changes before publishing, auditing content modifications, or tracking content evolution.

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。

Remove AI-generated code slop and clean up code style

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。

Clean up git branches marked as [gone] (deleted on remote but still exist locally). Use when you want to prune stale local branches, remove worktrees for deleted branches, or clean up after PR merges.

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。

Delete, redact, or archive project and global memories when the user says forget this, delete memory, remove that preference, do not remember, redact sensitive information, or retire stale memory.

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。

Audit UI, docs, or prose for AI-generated tells in design and copy, then fix approved findings. Use when the user says de-slop, slop check, "looks AI-generated", or wants copy humanized.

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。

Audit and rewrite content to remove 21 categories of AI writing patterns with a 43-entry replacement table

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。

Detects A/B chromatin compartments from balanced Hi-C contact matrices via eigenvector decomposition of the distance-normalized, Pearson-correlated cis matrix with cooltools (eigs_cis), then orients (phases) the compartment eigenvector against a GC or gene-density track so the active (A) sign is not arbitrary. Covers the eigenvector-is-a-choice problem (per-arm view_df to remove the centromere gradient; picking the eigenvector by max correlation with activity, not by eigenvalue), GC phasing with bioframe.frac_gc, resolution choice (100kb-1Mb), saddle plots and saddle_strength for compartmentalization strength, the cohesin-loss-strengthens-compartments result, subcompartments (SNIPER/Calder/dcHiC), and cross-condition compartment switching. Use when calling A/B compartments, computing E1/eigenvectors, phasing the eigenvector, building saddle plots, choosing a compartment resolution, quantifying compartment strength, or comparing compartmentalization across 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。

Handles batch effects in bulk RNA-seq via design-matrix inclusion (the correct path for DE), ComBat/ComBat-seq for visualization, SVA for unknown latent factors, RUVSeq for negative-control-gene-anchored unwanted variation, and limma::removeBatchEffect for plotting only. Encodes the Nygaard 2016 cardinal sin against testing on a batch-corrected matrix, the choice between SVA/RUVg/RUVs/RUVr, the confounding non-identifiability problem, the single-cell boundary (Harmony/MNN are NOT for bulk), and the Goh 2017 harmonization critique. Use when designing a DE analysis with batch structure, troubleshooting batch-dominated PCA, choosing ComBat vs ComBat-seq, handling unknown batch via SVA, integrating across studies, or deciding when (rarely) to subtract batch.

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。

Detects and removes doublets/aggregates from flow, spectral, and mass cytometry before clustering or quantification. Covers FSC-A vs FSC-H singlet discrimination (the Area-Height non-proportionality, not a 1D area gate), FSC-W/SSC width gating, CyTOF Gaussian discrimination parameters (Center/Offset/Width/Residual/Event_length) and DNA intercalator gating, and the residual heterotypic conjugates that survive scatter gating and masquerade as double-positive populations. Use when filtering aggregates before phenotyping, choosing a doublet method for flow vs CyTOF, or diagnosing a suspicious double-positive cluster.

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。

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, sequencing run, Cas9 lot, FBS lot), PCA + variance-decomposition diagnostic to decide if correction is needed, when correction harms biology by over-correcting condition into batch, limma removeBatchEffect for visualization-only correction, and relationship to multi-condition design matrices. Use when combining screens for joint analysis, when passage cohort confounds biology, when DepMap-style panels need Chronos with batch covariates, when picking ComBat vs RUV, or when correction harms biology and should be replaced with explicit covariate modeling.

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。

Call copy number variants with the GATK best-practices workflows — the somatic CNV pipeline (CollectReadCounts, DenoiseReadCounts with tangent normalization, ModelSegments, CallCopyRatioSegments) and the germline GATK-gCNV pipeline (DetermineGermlineContigPloidy, GermlineCNVCaller cohort/case mode, PostprocessGermlineCNVCalls). Covers panel-of-normals construction, AnnotateIntervals/FilterIntervals, allelic-count integration, and QS-based filtering. Use when integrating CNV calling into a GATK variant pipeline, calling rare germline CNVs from an exome cohort, deciding between the somatic and germline GATK workflows, or diagnosing why tangent normalization removed a real event or why gCNV output has low precision.

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。

Mark and remove PCR/optical duplicates using samtools fixmate and markdup. Use when preparing alignments for variant calling or when duplicate reads would bias 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。