Best research and science skills, page 125

Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files.

bioMate-AI/biomate-bioconductor-kb

A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.

bioMate-AI/biomate-bioconductor-kb

A robust and outlier-aware method for testing differential tissue composition from single-cell data.

bioMate-AI/biomate-bioconductor-kb

We present a statistical simulator, scDesign3, to generate realistic single-cell and spatial omics data, including various cell states, experimental designs, and feature modalities, by learning…

bioMate-AI/biomate-bioconductor-kb

Implements miscellaneous functions for interpretation of single-cell RNA-seq data.

bioMate-AI/biomate-bioconductor-kb

A post hoc cell type classification tool to fine-tune cell type annotations generated by any cell type classification procedure with semi-supervised learning algorithm AdaSampling technique.

bioMate-AI/biomate-bioconductor-kb

sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package.

bioMate-AI/biomate-bioconductor-kb

SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks.

bioMate-AI/biomate-bioconductor-kb

SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions.

bioMate-AI/biomate-bioconductor-kb

Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image.

bioMate-AI/biomate-bioconductor-kb

Defines a S4 class for storing data from single-cell experiments.

bioMate-AI/biomate-bioconductor-kb

SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data.

bioMate-AI/biomate-bioconductor-kb

The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging.

bioMate-AI/biomate-bioconductor-kb

SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data.

bioMate-AI/biomate-bioconductor-kb

Spatially-aware quality control (QC) software for both spot-level and artifact-level QC in spot-based spatial transcripomics, such as 10x Visium.

bioMate-AI/biomate-bioconductor-kb

standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data.

bioMate-AI/biomate-bioconductor-kb

Statial is a suite of functions for identifying changes in cell state.

bioMate-AI/biomate-bioconductor-kb

Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome.

bioMate-AI/biomate-bioconductor-kb

syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them.

bioMate-AI/biomate-bioconductor-kb

Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending.

bioMate-AI/biomate-bioconductor-kb

A first step in the data analysis of Mass Spectrometry (MS) based proteomics data is to identify peptides and proteins.

bioMate-AI/biomate-bioconductor-kb

This is an advanced version of TDbasedUFE, which is a comprehensive package to perform Tensor decomposition based unsupervised feature extraction.

bioMate-AI/biomate-bioconductor-kb

Variance-stabilizing transformations help with the analysis of heteroskedastic data (i.e., data where the variance is not constant, like count data).

bioMate-AI/biomate-bioconductor-kb

treekoR is a novel framework that aims to utilise the hierarchical nature of single cell cytometry data to find robust and interpretable associations between cell subsets and patient clinical end…

bioMate-AI/biomate-bioconductor-kb

This package enables the interpretation and analysis of results from a gene set enrichment analysis using network-based and text-mining approaches.

bioMate-AI/biomate-bioconductor-kb

SpatialFeatureExperiment (SFE) is a new S4 class for working with spatial single-cell genomics data.

bioMate-AI/biomate-bioconductor-kb

Zenith performs gene set analysis on the result of differential expression using linear (mixed) modeling with dream by considering the correlation between gene expression traits.

bioMate-AI/biomate-bioconductor-kb

Test willingness to pay before launching with proven pricing research methodologies.

guia-matthieu/clawfu-skills

Medicinal chemistry filters for compound triage. An agent skill from jaechang-hits/SciAgent-Skills.

jaechang-hits/SciAgent-Skills

面向真实业务决策的多平台事实核验 Skill。正式支持深知晓、深知晓（深度溯源）、豆包、腾讯元宝、DeepSeek 和通义千问，按用户输入动态选择 N≥1 个平台。完整采集原回答、引用、截图与页面存证，结构化比较关键事实，按需使用可信搜索逐点核验权威证据，并评估各平台表现。权威答案是核验产物之一，原始证据、冲突与证据边界全程可追溯。基础采集与对比无需 API…

aiskillstore/marketplace

Multi-source literature search, citation verification, MeSH search strategy, citation file management (.nbib/.ris/.bib conversion), and reference management (BibTeX, related articles, ID conversion)…

aiskillstore/marketplace

Simulate a Nature-style reviewer assessment from the referee perspective rather than an author rebuttal.

aiskillstore/marketplace

Codex adaptation of the OpenClaw Medical Skills library. An agent skill from aiskillstore/marketplace.

aiskillstore/marketplace

Work with a user's Semantic Scholar account to read Research Feeds, inspect private Library folders, add papers to folders, and resolve Semantic Scholar paper records from identifiers such as arXiv…

aiskillstore/marketplace

A skill your agent uses when running AlphaFold2 predictions on custom protein sequences, validating designed sequences via self-consistency, predicting binder-target complexes, or interpreting AF2…

lamm-mit/scienceclaw

Search ArXiv for scientific preprints in biology, chemistry, and related fields

lamm-mit/scienceclaw

Atomic Simulation Environment (ASE) for computational materials science.

lamm-mit/scienceclaw

Search NCBI BLAST for sequence homology and find similar sequences in biological databases

lamm-mit/scienceclaw

Small-molecule drug lookup by exact drug name or ChEMBL ID. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

ToolUniverse workflow — Clinical Guidelines. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Agentic materials discovery and DFT simulation framework using ASE, Quantum ESPRESSO, and Claude LLMs via LangGraph.

lamm-mit/scienceclaw

ToolUniverse workflow — Expression Data Retrieval. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

ToolUniverse workflow — Gwas Drug Discovery. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

ToolUniverse workflow — Gwas Trait To Gene. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Infinite platform integration for AI agent collaboration. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

Unified search across OSTI, Google Scholar, ArXiv, and corpus-search with deduplication and reciprocal rank fusion

lamm-mit/scienceclaw

Semi-empirical quantum chemistry with MOPAC. An agent skill from lamm-mit/scienceclaw.

lamm-mit/scienceclaw

OpenMM molecular dynamics engine for protein and ligand simulations.

lamm-mit/scienceclaw