用 Codex 或 Claude 帮你安装 复制这段 Prompt，粘贴到 Codex、Claude 或其他助手里，让它检查 Skill 页面并帮你完成安装。
直接命令不会经过审查 Prompt；运行前请先检查来源。
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想先保存到本地？可下载 SkillsMP 当前能够提供的文件。
Install and run the BD Rhapsody™ Sequence Analysis Pipeline (v3.0) on a shared cluster or remote Linux server with no root and no container runtime. Covers the self-contained install bundle, reference archives, FASTQ manifests, per-library YML generation, SLURM array execution, outputs, sample-tag demultiplexing, and the failure modes that cost hours — wrong Sample_Tags_Version on nuclei runs, uncapped Maximum_Threads, node-local scratch, and pinning a stale `latest` bundle.
Advanced single-cell multi-omics analysis including scRNA-seq, scCITE-seq, scATAC-seq, and TARGET-seq. Use when analyzing single-cell data, cell type identification, trajectory analysis, differential expression, UMAP/clustering, integrating protein and RNA modalities (TotalVI), or working with Scanpy, Seurat, scvi-tools. Includes workflows for MPN, hematologic malignancies, megakaryocyte biology.
Detects differential alternative splicing between conditions using rMATS-turbo (binomial LRT on junction counts), leafcutter (Dirichlet-multinomial GLM on intron clusters), MAJIQ V3 deltapsi/HET (Bayesian posterior on LSVs), SUPPA2 (empirical-null on TPM-derived PSI), or Shiba (junction-imbalance-corrected, 2025 SOTA at low coverage). Reports FDR-corrected significance and delta PSI effect sizes. Tools differ in statistical model, annotation dependence, calibration regime, and replicate-count requirements. Use when comparing splicing patterns between treatment groups, tissues, or disease states.
基于 SOC 职业分类
正在显示 SKILL.md
| name | scte |
| display_name | scTE |
| description | Quantify transposable element expression from single-cell RNA/ATAC-seq BAM files at locus or family level. |
| license | MIT |
| metadata | null |
scTE allocates aligned reads from single-cell RNA-seq or ATAC-seq BAM files to a unified gene + transposable element (TE) reference, producing a per-cell count matrix that contains both protein-coding genes and individual TE loci (or TE family aggregates). It uses prebuilt or custom genome indices that encode gene/exon coordinates alongside RepeatMasker-style TE annotations, and resolves the overlap between TE elements and gene bodies via configurable allocation modes (exclusive, inclusive, nointron). Output is a CSV table by default, or an AnnData .h5ad ready for Scanpy/Seurat workflows.
git clone https://github.com/JiekaiLab/scTE.git
cd scTE
python setup.py install
# Recommended companion tools
conda install -c bioconda samtools
pip install anndata h5py pysam numpy
Requires Python ≥ 3.6. Prebuilt indices for mm10, hg38, panTro6, macFas5, dm6, danRer11, and xenTro9 are bundled with the repository; custom genomes are built with scTE_build -te <BED> -gene <GTF> -o <prefix> -g <genome>.
CR:Z or CB:Z tags and UMIs in UR:Z or UB:Z tags.mm10.exclusive.idx, hg38.exclusive.idx, etc.) or custom index from GTF genes and BED TEs.scTE_build.scTE -i inp.bam -o out -x mm10.exclusive.idx --hdf5 True -CB CB -UMI UB
| Name | Default | Description |
|---|---|---|
-i | (required) | Input aligned BAM/SAM file. |
-o | (required) | Output file prefix. |
-x | (required) | Path to prebuilt or custom genome index (.idx). |
-p | 1 | Number of threads (~10 GB RAM per thread). |
--hdf5 | False | Emit .h5ad AnnData instead of CSV when True. |
-CB | CR | Cell barcode BAM tag name, or False to disable. |
-UMI | UR | UMI BAM tag name, or False to disable. |
-m / --mode | exclusive | TE/gene overlap allocation: exclusive, inclusive, or nointron. |
--hdf5 True) count matrix with cells as rows and genes/TEs as columns..h5ad file directly loadable in Scanpy (sc.read_h5ad) or convertible to Seurat via SeuratDisk::Convert.-p on modest systems.CB:Z/UB:Z, STARsolo uses CR:Z/UR:Z — wrong flags silently produce empty matrices.-m inclusive to count both.scTE_build.samtools sort + samtools index) for best performance; very large BAMs (>50 GB) may take hours.He, J. et al. (2021). "scTE: identifying the activity of transposable elements at single-cell resolution." Nature Communications 12, 1456. DOI: 10.1038/s41467-021-21808-x.