sequencing-base-masks

Plugin sequencing-base-masks from marketplace kaiser-skills in CodingKaiser/kaiser-skills. Commands read from the repo's manifest — 1 month ago.

Skills (11)

• bfabricpy

  Python interface to the B-Fabric laboratory information management system. Use when working with B-Fabric API for CRUD operations on samples, datasets, workunits, resources, or building B-Fabric applications and scripts.

• marimo-notebook

  Write a marimo notebook in a Python file in the right format.

• pixi-package-manager

  Fast, reproducible scientific Python environments with pixi - conda and PyPI unified

• plotly-compact

  Compact Plotly visualization patterns. Express for quick plots, Graph Objects for control.

• python-cli-patterns

  CLI application patterns for Python. Triggers on: cli, command line, typer, click, argparse, terminal, rich, console, terminal ui.

• python-style-guide

  Comprehensive Python programming guidelines based on Google's Python Style Guide. Use when you needs to write Python code, review Python code for style issues, refactor Python code, or provide Python programming guidance. Covers language rules (imports, exceptions, type annotations), style rules (na

• r-development

  Modern R development practices emphasizing tidyverse patterns (dplyr 1.1 and later, native pipe, join_by, .by grouping), rlang metaprogramming, performance optimization, and package development. Use when you needs to write R code, create R packages, optimize R performance, or provide R programming g

• r-single-cell-plotting

  R plotting conventions for Seurat/scRNA-seq: UMAP square plots (aspect.ratio=1, raster=FALSE), polychrome cluster colors, DimPlot/FeaturePlot settings, saving 300 DPI PNG, volcano plots with EnhancedVolcano, statistical comparisons with rstatix/ggpubr.

• rmd-formatting

  R Markdown formatting patterns: chunk display strategies (include=FALSE + inline R vs results='asis'), table rendering with knitr::kable, header hierarchy with tabsets, downloadable file embedding, and what to avoid (cat/print in visible chunks).

• sequencing-base-masks

  Sequencing read requirements and bcl2fastq base masks for 10x Genomics libraries: chemistry-specific BasesMaskCR values, ATAC I2 barcode requirement (capital I not lowercase y), Visium FFPE vs frozen R2 length difference.

• shell-scripting

  Specialized knowledge of Bash and Zsh scripting, shell automation, command-line tools, and scripting best practices. Use when the user needs to write, debug, or optimize shell scripts, work with command-line tools, automate tasks with bash/zsh, or asks for shell script help.