Results for “cell-type-annotation”

This skill should be used when working with single-cell omics data analysis using scvi-tools, including scRNA-seq, scATAC-seq, CITE-seq, spatial transcriptomics, and other single-cell modalities. Use this skill for probabilistic modeling, batch correction, dimensionality reduction, differential expression, cell type annotation, multimodal integration, and spatial analysis tasks.

Notebook Cell References

Use to convert references to Cell Press author–date style — in-text "(Smith et al., 2021)", an alphabetical reference list by first author with full author lists, journal names spelled out. This is the OPPOSITE of Science's numbered-by-appearance style.

Apply the scGPT single-cell foundation model (Cui 2024) to annotate and embed cells — zero-shot and fine-tuned cell-type annotation, gene/cell embeddings, batch integration, and gene-regulatory / perturbation inference from AnnData. Use when annotating cell types with a pretrained foundation model, generating scGPT embeddings, integrating batches with a transformer, or running zero-shot single-cell inference on an h5ad. For probabilistic latent models (scVI/scANVI) prefer alterlab-scvi-tools; for the standard QC→cluster→UMAP→DE pipeline prefer alterlab-scanpy; for the AnnData data structure itself prefer alterlab-anndata; for protein language models prefer alterlab-esm. Part of the AlterLab Academic Skills suite.

Annotate the outline with where to mention specific brand products. Designed-in at outline time so product callouts feel natural in the draft, not bolted on.

Add visual callouts like rectangles, arrows, and labels to screenshots, diagrams, and images using PIL/Pillow, with support for animated GIF annotations.

Use when annotating VCF files with flanking sequence information (INFO/FS tag) or masking regions/variants in flanking sequences.

Use when tightening annotations in existing TypeScript, removing avoidable any or assertions, improving changed-file types, or reducing compiler errors without broad refactoring.

Use to structure a Cell Article and hold its length — Summary, Introduction, Results, Discussion, STAR Methods, figure legends, references — with main-text length and display-item budgets, and Results subheadings driving the single arc.

Use when you need to annotate BAM alignments with a two-character tag based on overlaps with BED, GFF, or VCF annotation files, such as labeling reads by feature class or interval source.

Search Copy

Annotates VCF variants using Ensembl VEP, ClinVar, and gnomAD, ranks them by predicted impact, and generates a reproducible report.

Tighten annotations in existing Python code with a focused, low-churn workflow based on Honnibal's tighten-types skill. Use to improve changed files, remove avoidable Any, make container and return types precise, or reduce type-checker errors without broad refactoring.

Predicts gene and transcript structure from a DNA sequence using the hosted Genomic Intelligence API, producing a report and JSON output.

Use when writing or editing typed Python scripts, parsing untyped input, choosing lightweight data shapes, or resolving common checker errors without project-scale type-system research.

Capture, organize, and retrieve notes efficiently using structured formats, tagging, and file management for meetings, ideas, research, and daily logs. Use when the user requests note taking or provides relevant inputs for this workflow.

Use to build Cell's data and code deposition plan and the Data and Code Availability statement that lives inside STAR Methods Resource Availability — approved repositories, accessions/DOIs at submission, and Cell's three-bullet availability format with Mendeley Data as Elsevier's default.

TypeScript Utility Types

A mention input component for @mentions with dropdown suggestions, supporting both text and textarea modes

Set up and manage data labeling workflows using manual annotation tools, semi-automated pipelines, active learning, and programmatic weak supervision. Use when the user requests data labeling or provides relevant inputs for this workflow.

Use to lock the single narrative arc before drafting — converts a set of correct results into one Cell-shaped story that runs hypothesis → mechanism → significance, not a list of experiments.

Use when answering difficult or disputed TypeScript questions about assignability, inference, narrowing, variance, generics, conditional or mapped types, declarations, or compiler-option semantics.

Use when deciding which cell-* sub-skill to invoke next, or when sequencing a manuscript from significance test through reviewer rebuttal for Cell (Cell Press). Routes — it does not replace — the specialized skills.

Ensure C# types are documented with XML comments following best practices for summaries, parameters, returns, and exceptions.

Use to write Cell's Summary — a single unstructured paragraph of ≤ ~150 words that conveys the complete story, the mechanism, and the broad significance, quantified and readable by a general life-scientist. Late-stage polish.

Creates Keynote-style presentations as single-page HTML slides with keyboard navigation, fade transitions, and a clean, minimal layout.

Implements standard document attachments, links, and notes on custom Business Central tables. Creates setup fields for visibility control, extends Attachment Document Type enum, generates event subscribers (OnBeforeDrillDown, OnAfterOpenForRecRef, OnAfterInitFieldsFromRecRef) in attachment management codeunit, adds table lifecycle triggers for orphan prevention on delete/rename, and extends card and list pages with both legacy and modern factboxes. Handles SubPageLink configuration, control ID mapping for Links (Control1900383207) and Notes (Control1905767507) factboxes. Use when adding attachments to custom tables, implementing document management, enabling factboxes for documents, creating attachment integration on entities, adding links and notes to records, or preventing orphan attachment records on table operations.

Design and format publication-quality tables: column order, row grouping, notes, precision, reproducibility.

Creates minimal, monochrome Keynote-style presentations with arrow-key navigation, accent lines, and mono lists.

Write and debug spreadsheet formulas (Excel/Google Sheets), pivot tables, and array formulas; translate between dialects; use when users need working formulas with examples and edge-case checks.

Opens plans and HTML artifacts in a local browser canvas where the human annotates elements, chats, and approves or requests changes without leaving the page. Use when presenting a plan for review, or when feedback like "move this, change that" is easier pointed at than typed.