8,135 件 ・ 関連度順
Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. Here we present a workflow that describes how exact binding sites can be defined from iCLIP data. The package provides functions for binding site definition and result visualization. For details please see the vignette.
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。
Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. Methods are also provided to assign cells to inferred clones and explore differences in gene expression between clones. These methods can flexibly integrate information from imperfect clonal trees inferred based on bulk exome-seq data, and sparse variant alleles expressed in scRNA-seq data. A flexible beta-binomial error model that accounts for stoc
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。
Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). The following nucleases are supported: SpCas9, AsCas12a, enAsCas12a, and RfxCas13d (CasRx). The available on-target cutting efficiency scoring methods are RuleSet1, Azimuth, DeepHF, DeepCpf1, enPAM+GB, and CRISPRscan. Both the CFD and MIT scoring methods are available for off-target specificity prediction. The package also provides a Lindel-derived score to predict the probability of a gRNA to
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。
This package provides the visualization of bayesian network inferred from gene expression data. The networks are based on enrichment analysis results inferred from packages including clusterProfiler and ReactomePA. The networks between pathways and genes inside the pathways can be inferred and visualized.
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。
lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. This package can be used to provide a high-level summary of cell-type colocalization in multiplexed imaging data that has been segmented at a single-cell resolution.
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。
Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed fu
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。
MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. It uses scoring matrices to be used in these pairwise distance calcualtions which can be adapted to any scoring for DNA or AA characters. E.g. by using literal distances MSA2dist calculates pairwise IUPAC distances.
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。
Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. Functions included in the package allow the user to learn supervised mutational signatures from their data and apply them to new data. The methodology is based on the one described in Afsari (2021, ELife).
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。
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.
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。
A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins. With this respect the huge number of experimental mass spectra typically have to be assigned to theoretical peptides derived from a sequence database. Search engines are used for this purpose. These tools compare each of the observed spectra to all candidate theoretical spectra derived from the sequence data base and calculate a score for each comparison. The observed spectrum
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。
topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and
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。
Installs a self-contained conda instance that is managed by the R/Bioconductor installation machinery. This aims to provide a consistent Python environment that can be used reliably by Bioconductor packages. Functions are also provided to e
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。
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.
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。
MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. The repertoire of antigens presented in a given genetic background largely depends on the sequence of the encoded MHC molecules, and thus, in humans, on the highly variable HLA (human leukocyte antigen) genes of the hyperpolymorphic HLA locus. More than 28,000 different HLA alleles have been reported, with significant differences in allele frequencies between human populations worldwide
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。
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. The duplication modes are i. segmental duplication (SD); ii. tandem duplication (TD); iii. proximal duplication (PD); iv. transposed duplication (TRD) and; v. dispersed duplication (DD). Transposon-derived duplicates (TRD) can be further subdivided into rTRD (retrotransposon-derived duplication) and dTRD (DNA transposon-derived duplication). If users want a s
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。
This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated me
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。
This package is a implementation of biclustering ensemble method MoSBi (Molecular signature Identification from Biclustering). MoSBi provides standardized interfaces for biclustering results and can combine their results with a multi-algorithm ensemble approach to compute robust ensemble biclusters on molecular omics data. This is done by computing similarity networks of biclusters and filtering for overlaps using a custom error model. After that, the louvain modularity it used to extract biclus
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。
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualizat
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。
Expert knowledge for Azure Repos development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, and integrations & coding patterns. Use when managing Git/TFVC repos, branch policies/PR checks, TFVC→Git migrations, large files, or security scanning, and other Azure Repos related development tasks. Not for Azure DevOps (use azure-devops), Azure Pipelines (use azure-pipelines), Azure Boards (use azure-boards), Azure Artifacts (use azure-artifacts).
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。
Expert knowledge for Azure Lab Services development including troubleshooting, best practices, decision making, architecture & design patterns, limits & quotas, security, configuration, integrations & coding patterns, and deployment. Use when configuring lab plans, VM templates/schedules, VNet-integrated labs, GPU/nested virtualization, or Canvas/Teams integration, and other Azure Lab Services related development tasks. Not for Azure DevTest Labs (use azure-devtest-labs), Azure Virtual Machines (use azure-virtual-machines), Azure Virtual Desktop (use azure-virtual-desktop).
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。
已有功能的需求变更闭环（门禁式七步）。触发硬条件：要改的功能已经实现并跑起来了。当用户说"改需求""需求变更""调整交互""改功能""重构流程"，或改动容易散到多个文件、碰到鉴权/存储/配置/权限、需要可靠验证 + 回滚方案时使用。流程：锁 scope 写 change brief → 从代码确认当前行为（不靠记忆和假设）→ 影响面与风险评估 + 回滚计划 → 提出新设计等用户批准（**未获批准绝不动代码**）→ 小而局部的 diff → 跑固定回归清单 → 更新文档和决策日志。产出：change brief + 代码 diff + 回归记录 + decision log。不适用于：全新功能从零做（走 issue-pool → page-solution-design（有界面时）→ backend-logic-design（有规则需讨论时）→ prd-test-writer）、只改视觉样式不动任何逻辑（按已有界面直接调整）、新想法还没定要不要做（先用 issue-pool 入池）、写 PRD/测试用例（用 prd-test-writer）、提交推送发版（用 git-push）。注意：本 skill 的七步流程通用于任何项目，但 scripts/impact_scan.sh 与 references/chrome-extension-regression-example.md 是 Chrome 扩展示例；通用回归使用 references/regression-checklist.md，按项目实际选择检查。
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。
Keep README files current with project changes. Use when project structure changes, features added, or setup instructions modified. Suggests README updates based on code changes. Triggers on significant project changes, new features, dependency 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。
Detect exposed secrets, API keys, credentials, and tokens in code. Use before commits, on file saves, or when security is mentioned. Prevents accidental secret exposure. Triggers on file changes, git commits, security checks, .env file modifications.
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 this skill when the user asks to "analyze my content", "learn my writing style", "research competitors", "find content angles", "improve my blog", "write like me", "embody my brand voice", or mentions content strategy, voice analysis, competitive research, or iterative content improvement.
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。