75 件 ・ 関連度順
概要と使いどころ
当用户明确要求"标书QC/质量控制/润色前质检/引用真伪核查/篇幅与结构检查"时使用。对 NSFC 标书进行只读质量控制：并行多线程独立检查文风生硬、引用假引/错引风险、篇幅与章节分布、逻辑清晰度等，最终输出标准化 QC 报告；中间文件默认归档到 `project_root/.bensz-api/task-{yyyymmdd-hhmm}-{简短描述}/nsfc-qc/{yyyy-mm-dd-hh-mm}/`，并兼容 legacy `.nsfc-qc/` 读取/清理。
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。
当用户给出期刊/杂志名并希望了解投稿要求、投稿形式/格式清单、期刊官网信息、社区评价、审稿速度、费用、文章类型、格式细节或“这个 journal 怎么投/是否靠谱/投稿指南调研”时必须使用。联网核验期刊官网与社区评测，默认把全部中间文件隔离到当前工作目录的 `.bensz-api/task-{yyyymmdd-hhmm}-{简短描述}/paper-know-journal/`，最终只交付 `KnowJournal-{杂志名}.md`。⚠️ 不适用：用户要根据 manuscript 选择投稿期刊（用 paper-select-journal）、写论文正文、下载全文 PDF，或只问一个无需成稿的简单事实。
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。
Fixes broken line wrapping in Claude Code exported .txt conversation files — rebuilds tables, paragraphs, paths and tool calls hard-wrapped at a fixed width. Use for an export (YYYY-MM-DD-HHMMSS-*.txt) with broken tables, split paths, or mangled tool output, or "fix export" / "make export readable". Not for a live web conversation (use read-claude-web-conversation) or session history (use read-claude-code-history).
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。
Estimates tumor fraction (the genome-wide proportion of cfDNA molecules that are tumor-derived, the cfDNA analogue of bulk-tumor purity) from shallow whole-genome sequencing with ichorCNA, an HMM over 1 Mb bins that jointly EM-estimates tumor fraction, ploidy, and subclonal prevalence over a normal/ploidy grid. Encodes the load-bearing reframes: tumor fraction is the quantity that travels across assays and is NOT mutation VAF (clonal-het VAF approximately TF/2), CNA-based estimation has a hard ~3 percent limit-of-detection floor, and near-diploid or copy-neutral-LOH genomes return a falsely low value. Selects the estimator by data type (sWGS to ichorCNA, deep panel to max-VAF, methylation to deconvolution, sub-3 percent to fragmentomics or methylation). Use when quantifying tumor burden from a liquid biopsy, picking a tumor-fraction estimator for a given assay, or reconciling a TF estimate against a panel VAF.
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。
Identifies differential m6A methylation between conditions from MeRIP-seq paired IP/input data using exomePeak2 (GC-bias-aware differential via its bam_ip/bam_input control + bam_treated_ip/bam_treated_input treatment arms), QNB beta-binomial, MeTDiff HMM, and RADAR, plus the paired-symmetric edgeR/DESeq2-on-peak-counts route when batch/lot covariates need fixed-effect handling that exomePeak2's API does not accept. Covers paired vs unpaired vs interaction designs, batch confounding and per-lot meta-analysis, the stoichiometry-vs-expression-vs-IP-efficiency confound, and effect-size filtering against under-powered N=2 designs. Use when comparing m6A across two or more conditions, choosing between exomePeak2/QNB/RADAR/MeTDiff for a design, handling batch confounding when exomePeak2's API is too rigid, distinguishing real hyper/hypo-methylation from expression shifts, applying effect-size thresholds, or planning orthogonal stoichiometry validation (GLORI/SAC-seq/m6Anet mod_ratio).
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。
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.
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 protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.
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 horizontal gene transfer (HGT / LGT) using compositional methods (GC%, codon usage, tetranucleotide z-scores via SIGI-HMM, AlienHunter, IslandViewer 4, IslandPath-DIMOB), phylogenetic-incongruence methods (AvP, HGTphyloDetect, ALE / GeneRax / AleRax reconciliation, RANGER-DTL), and BLAST-distribution methods (HGTector v2, DarkHorse, Alien Index). Use when screening prokaryote genomes for genomic islands and HGT events, distinguishing HGT from incomplete lineage sorting / differential gene loss / hybridization, mapping donor lineages via phylogenetic placement, separating eukaryotic HGT from contamination, ruling out gBGC as a false signal, or quantifying DTL rates with ALE/GeneRax on bacterial trees.
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 single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.
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 somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
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。
Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.
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。
Analyzes differential transcript usage (DTU) and isoform switches with functional consequence prediction (NMD via 50nt rule, ORF disruption, protein domain loss/gain, signal peptide changes, IDR alterations, coding-potential shifts). Tools include IsoformSwitchAnalyzeR v2 (auto-selects satuRn for >5 reps else DEXSeq), the manual DRIMSeq -> DEXSeq/satuRn -> stageR DTU pipeline, and fishpond/swish for inferential-uncertainty-aware DTE. Distinguishes DTU from DGE and DTE; integrates external annotators (CPC2, Pfam, SignalP, IUPred2A or DeepTMHMM). Use when investigating how splicing differences alter protein function or trigger NMD-mediated degradation.
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 somatic CNVs from WES/WGS/targeted BAMs (CNVkit v0.9.x). Bin coverage in target/antitarget regions, normalize vs reference, segment with CBS/HMM, call amps/dels, scatter/diagram plots, purity/ploidy, VCF/SEG export. CLI plus Python API (cnvlib). Use GATK CNV for deep WGS with population controls; use CNVkit for targeted/exome where antitarget bins matter.
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。
Annotate prokaryotic genomes (bacteria, archaea, viruses) via Prokka's BLAST/HMM pipeline. Identifies CDS, rRNA, tRNA, tmRNA, signal peptides against Pfam, TIGRFAMs, RefSeq. Outputs GFF3, GenBank, FASTA, TSV. Use PGAP for NCBI GenBank submission; Bakta for faster NCBI-compatible annotation.
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。
Annotate bacterial and archaeal genomes and plasmids with Bakta's Prodigal/HMM/diamond pipeline. Identifies CDS, ncRNA, tRNA, rRNA, tmRNA, sORFs, CRISPR arrays, oriC/oriV/oriT, and gaps against a curated UniRef-derived database. Produces NCBI-compatible GFF3, GenBank, EMBL, JSON, FASTA, TSV, and a circular genome plot. Use Prokka for legacy pipelines or non-bacterial kingdoms; PGAP for NCBI GenBank submission.
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。
Think and work like an expert Behavioral Ecologist. Use when a task calls for Behavioral Ecologist judgment. Reasons from versioned ethograms, Altmann focal/scan sampling, and activity budgets; scores with BORIS (Cohen’s κ), analyzes sequences with Markov/HMM tools, runs sham-controlled playbacks under ARRIVE 2.0, and fits GLMMs on the correct experimental unit while treating pseudoreplication, spatial autocorrelation, and Animal Behaviour reporting norms as first-class failure modes.
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 single-nucleotide crosslink (CL) sites in CLIP-seq data using truncation patterns (iCLIP/eCLIP CITS), crosslink-induced mutations (HITS-CLIP CIMS deletions, PAR-CLIP T-to-C), or HMM/kernel-density methods (PureCLIP, PARalyzer, CTK). Use when single-nucleotide resolution is required for motif registration (mCross), allele-specific binding (BEAPR), variant-effect prediction, or comparing crosslink chemistry across CLIP variants.
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。
Normalize read-depth copy-ratio profiles and segment them into copy-number regions using circular binary segmentation (CBS, DNAcopy), hidden Markov models, HaarSeg, and fused-lasso methods. Covers GC-content, mappability, and replication-timing (wave-artifact) bias correction, panel-of-normals/PCA denoising, diploid-baseline centering, and algorithm selection by sequencing depth and event size. Use when choosing a segmentation algorithm, correcting depth bias, diagnosing oversegmentation or a mis-centered baseline, tuning CBS or HMM parameters, or understanding why a downstream CNV caller produced fragmented or shifted segments.
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 protein-RNA binding sites from CLIP-seq BAM with CLIPper, PureCLIP, Skipper, Piranha, omniCLIP, CTK, CLAM, or Paraclu. Use when choosing between coverage-based, HMM-based, beta-binomial window-based, and crosslink-site-based peak callers; applying ENCODE eCLIP thresholds (log2 IP/SMInput >= 3, -log10 p >= 3); deciding when SMInput is mandatory; or reconciling peak-set discordance between callers for the same RBP.
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 somatic and germline copy number variants from targeted, exome, and whole-genome sequencing with CNVkit, a read-depth caller that combines on-target and off-target (antitarget) coverage. Covers panel-of-normals construction, flat-reference tumor-only calling, hybrid/amplicon/WGS modes, CBS vs HMM segmentation selection, purity-aware integer calling, and reconciliation against GATK and allele-specific callers. Use when calling CNVs from hybrid-capture panels or exomes, deciding whether CNVkit (depth-only) is the right tool versus an allele-specific caller, building a panel of normals, diagnosing flat-reference false positives, or interpreting log2 ratios into copy-number states.
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。
Reconstruct ancestral states at internal phylogenetic nodes for sequences (PAML codeml, IQ-TREE --ancestral, GRASP, FastML), discrete traits (corHMM hidden-rate Markov, ape::ace, phytools::make.simmap stochastic mapping, BayesTraits), and continuous traits (phytools::fastAnc, geiger Brownian/OU, RPANDA). Use when designing constructs for ancestral protein resurrection, tracing trait evolution along a tree, performing stochastic character mapping, testing models of trait evolution (BM vs OU vs EB), inferring ancestral genome content via Dollo or DTL reconciliation, or quantifying ancestral-state uncertainty for downstream comparative analyses.
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。
Use when writing, reviewing, or optimizing CUDA kernels targeting sm_120a (RTX 5090 / Consumer Blackwell, GB202) in the imp inference engine. Triggers on CUDA/PTX kernel code, shared-memory layout, bank conflicts, tensor-core MMA (mxf4nvf4, tf32, 3xTF32/3xFP16), GEMV/GEMM/attention/quantization/GDN-scan kernels, decode tok/s under expected, kernel emitting HMMA instead of mxf4nvf4, occupancy, register pressure, __launch_bounds__, spills, PDL. Pair with `benchmark-cuda` for measurement and `check-degeneration` after hot-path changes.
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。
Fit hidden Markov models using the Baum-Welch (EM) algorithm with model selection, Viterbi decoding for state sequences, and forward-backward probabilities. Use when observations are generated by unobservable latent states, you need to segment a time series into latent regimes (market regimes, speech phonemes, biological sequences), compute sequence probabilities, decode the most likely hidden state path, or compare models with different numbers of hidden states.
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。
Use when a task needs the judgment of an electric-motor and power-tool repairer — reading a megohmmeter/polarization-index test to catch a winding fault before failure, deciding rewind vs. replace on a failed induction motor, isolating a bearing fault from a broken-rotor-bar fault, judging brush/commutator wear on a universal motor, or evaluating whether a rewind was actually done to spec.
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。