304 件 ・ 関連度順
概要と使いどころ
Use when deciding which aejmic-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an American Economic Journal: Microeconomics (AEJ: Micro) submission. Routes — it does not replace — the specialized skills.
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 deciding which aejmac-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an American Economic Journal: Macroeconomics (AEJ: Macro) submission. Routes — it does not replace — the specialized skills.
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 deciding which advmat-* sub-skill to invoke next, or when sequencing manuscript work from scope-fit through revision for an Advanced Materials (Adv. Mater.) manuscript. Routes — does not replace — the specialized skills.
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 deciding which asq-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an Administrative Science Quarterly (ASQ) manuscript. Routes — it does not replace — the specialized skills.
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 deciding which aejpol-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an AEJ: Economic Policy manuscript. Routes — it does not replace — the specialized skills.
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 deciding which aeja-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an American Economic Journal: Applied Economics (AEJ: Applied) submission. Routes — it does not replace — the specialized skills.
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 auditing an ACM CCS submission for HotCRP readiness, dual-cycle abstract registration and full-paper deadlines, the 12-page ACM sigconf body, anonymization, the ethics considerations appendix, artifact-availability posture, dual-submission policy, per-cycle submission caps, desk-reject triggers, and final-week sequencing.
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 auditing an ACM MM (ACM Multimedia) submission for OpenReview readiness — thematic-area choice, the 6-8 page ACM sigconf budget, references-only overflow, double-blind anonymity versus the single-blind Reproducibility/Open-Source/Dataset tracks, supplementary media, dual submission, desk-reject triggers, and last-week sequencing.
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 deciding which amr-* sub-skill to invoke next, or when sequencing a theory-building manuscript from theoretical-puzzle framing through developmental-review revision for an Academy of Management Review (AMR) submission. Routes — does not replace — the specialized skills.
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 deciding which acr-* sub-skill to invoke next, or when sequencing manuscript work from fit positioning through rebuttal for 《会计研究》 (Accounting Research). Routes — does not replace — the specialized skills.
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 deciding which aos-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an Accounting, Organizations and Society (AOS) manuscript. Routes — it does not replace — the specialized skills.
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 deciding which amann-* sub-skill to invoke next, or when sequencing a comprehensive review article from topic selection through revision for an Academy of Management Annals (Annals) submission. Routes — it does not replace — the specialized skills.
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 deciding which amj-* sub-skill to invoke next, or when sequencing manuscript work from topic selection through rebuttal for an Academy of Management Journal (AMJ) manuscript. Routes — it does not replace — the specialized skills.
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。
Basecalls raw Oxford Nanopore signal (POD5/FAST5) into reads with Dorado, choosing the chemistry-matched model and accuracy tier (fast/hac/sup), requesting modified bases (5mCG_5hmCG, 6mA, m6A) at basecall time, and handling duplex, demultiplexing, trimming, and HERRO read correction. Covers why the model+version is an irreversible analysis decision, why methylation cannot be recovered later, and why downstream polish/variant models must match the basecaller. Use when converting POD5/FAST5 to reads, picking a Dorado model for R9/R10 or RNA004, enabling methylation calling, basecalling duplex, demultiplexing barcoded runs, or correcting reads for assembly.
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。
Calls germline small variants (SNPs and indels) from Oxford Nanopore and PacBio HiFi long reads with Clair3, a two-stage (pileup + full-alignment) deep-learning caller, selecting the chemistry- and basecaller-version-matched model, enabling read-based phasing, and benchmarking against GIAB with stratification. Covers why the model string is the experiment (no auto-detection, silent degradation on mismatch), why ONT homopolymer/STR indels are the residual error whole-genome F1 hides, and the somatic/trio/RNA boundary to the ClairS/Clair3-Trio family. Use when calling germline SNVs/indels from ONT or HiFi BAMs, choosing a Clair3 model, phasing variants, or benchmarking long-read calls.
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。
Phases small variants, SVs, and methylation from Oxford Nanopore and PacBio long reads (read-backed/physical phasing) with WhatsHap, LongPhase, or HiPhase, and haplotags the BAM (HP/PS tags) for allele-resolved downstream analysis. Covers why phase blocks break at het-sparse gaps (read length x heterozygosity), why phasing the VCF is useless until the BAM is haplotagged, the GT-pipe/PS and read HP/PS tag spec, reporting block N50 with switch error, the diploid-assumption/CNV/haploid-region traps, trio phasing as the gold standard, and the boundary to statistical panel phasing. Use when phasing long-read variants, haplotagging reads for allele-specific methylation/expression or phased SVs, choosing WhatsHap vs LongPhase vs HiPhase, trio phasing, or assessing phasing quality.
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。
Decides how to preprocess plasma cfDNA sequencing data so the recoverable signal survives - library-prep-aware fragment expectations (dsDNA vs ssDNA/adaptase prep), UMI/duplex consensus with fgbio (ExtractUmisFromBam, GroupReadsByUmi --strategy paired for duplex, CallMolecularConsensusReads vs CallDuplexConsensusReads, FilterConsensusReads min-reads "total s1 s2"), the align->group->consensus->RE-align ordering, and the cfDNA dedup trap where naive coordinate dedup collapses nucleosome-coincident independent molecules. Covers when single-strand consensus suffices vs when duplex is mandatory, the singleton/sensitivity tax at low input, and reading the insert-size histogram as a pre-analytical QC instrument. Use when processing plasma cfDNA reads before fragmentomics, ctDNA mutation calling, or tumor-fraction estimation.
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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。
Assembles microbial-community sequencing into metagenome-assembled genomes (MAGs) with metaFlye (ONT), metaSPAdes/MEGAHIT (Illumina), and hifiasm-meta/metaMDBG (PacBio HiFi), then recovers genomes via multi-binner consolidation (MetaBAT2, MaxBin2, CONCOCT, SemiBin2, VAMB -> DAS_Tool) and QCs them against MIMAG with CheckM2, GUNC, and GTDB-Tk. Covers why a metagenome is not a genome (uneven coverage, micro-diversity, strain collapse to consensus), differential-coverage binning, co-assembly vs per-sample, the rRNA-operon collapse that fails short-read MAGs, and strain resolution with inStrain. Use when reconstructing genomes from a microbiome, soil, ocean, or gut community, recovering MAGs, or resolving strain-level variation.
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。
Discovers, classifies, filters, and quantifies full-length transcript isoforms from PacBio Iso-Seq/Kinnex (HiFi) and Oxford Nanopore (cDNA/direct-RNA) long reads, using the isoseq+pigeon pipeline, SQANTI3, and ONT tools (IsoQuant, FLAIR, Bambu, StringTie2). Covers why a novel isoform is an artifact until proven otherwise (RT template-switching, intra-priming, and 5' degradation manufacture junctions and truncations), the SQANTI3 structural categories and their trust order, the Kinnex skera-split step, orthogonal CAGE/poly-A/short-read-junction validation, and why long-read isoform quantification needs EM. Use when building a full-length isoform catalog, classifying/filtering long-read transcripts, running Iso-Seq or ONT cDNA/dRNA analysis, or judging novel-isoform reliability.
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。
Designs genomics experiments so technical nuisance variation (batch, lane, plate, flow cell, operator, reagent lot, processing day) is balanced against the biological variable of interest and therefore estimable rather than confounded, using constrained sample-to-batch assignment (designit, OSAT), the confounder/mediator/collider distinction, and the principle that no post-hoc correction recovers a fully confounded design. Covers detecting hidden batches with surrogate variable analysis, a decision table for downstream correction (ComBat-seq, RUVSeq, SVA) whose execution is deferred to differential-expression/batch-correction, and reproducibility metadata. Use when assigning samples to sequencing batches/lanes/plates, avoiding batch-condition confounding, deciding whether a design is salvageable by correction, choosing a correction method, or estimating the number of hidden batches. For the experimental unit, randomization, and blocking concepts see experimental-design/randomization-blocking.
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Structures biological experiments so inference is valid by construction, covering Fisher's principles (randomization, replication, local control), the experimental-vs-observational unit distinction and pseudoreplication (Hurlbert 1984; Lazic 2018), randomization mechanics (complete, restricted, stratified, rerandomization, run-order), blocking layouts (randomized complete block, Latin square, incomplete block), factorial designs and interactions, and the split-plot/nested error strata hidden inside multi-batch genomics. Use when deciding the experimental unit and what counts as a replicate, planning randomization and run order, choosing a blocked/factorial/split-plot/nested layout, avoiding pseudoreplication in cell-culture or animal studies, or specifying the random-effects structure of the analysis model. For assigning samples to sequencing batches/lanes/plates and batch-effect correction see experimental-design/batch-design; for regulated clinical-trial randomization see clinical-biostatistics.
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Profiles a genome from raw reads BEFORE assembly with a k-mer spectrum (KMC or Jellyfish histogram), then models it with GenomeScope2 to estimate genome size, heterozygosity, repeat content, and ploidy, and Smudgeplot to infer ploidy from heterozygous k-mer pairs (diploid AB vs triploid AAB vs tetraploid AABB). Covers choosing k via Merqury best_k.sh, the k-mer-coverage vs sequencing-coverage confusion, reading het/repeat/contamination/organelle peaks, why noisy ONT must not be used for counting, and how the estimate becomes the NG50 denominator, the Flye -g value, the hifiasm --hom-cov/purge setting, and the 1.5-2x-too-big haplotig sanity check. Use when starting any de novo assembly, deciding whether short reads can work, estimating genome size for an unknown organism, diagnosing ploidy, or sanity-checking an assembly's size against expectation.
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。
Download raw sequencing reads from NCBI SRA using sra-tools (prefetch, fasterq-dump, vdb-validate) or the ENA mirror. Use when pulling FASTQ for SRR/ERR/DRR accessions, deciding between SRA-direct, ENA mirror, or AWS/GCP cloud mirror (STRIDES), handling --include-technical for 10x and other single-cell records, validating with MD5/vdb-validate, navigating SRR/SRX/SRS/SRP/PRJNA hierarchy, or finding accessions via pysradb. Encodes SRA cloud-egress economics, the fasterq-dump uncompressed-scratch trap, and the --max-size default that silently truncates large prefetches.
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。