GitHub organization
Agent skills by bioMate-AI
- skills
- 112
- repository
- 1
Repositories by bioMate-AI
Skills by bioMate-AI, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 1 | This package provides a client for the Bioconductor AnnotationHub web resource. | bioMate-AI/ | 804 | — | ~2.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 2 | ASURAT is a software for single-cell data analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 3 | We propose an Asymmetric Within-Sample Transformation (AWST) to regularize RNA-seq read counts and reduce the effect of noise on the classification of samples. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 4 | The Bandle package enables the analysis and visualisation of differential localisation experiments using mass-spectrometry data. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5 | Implements a variety of methods for batch correction of single-cell (RNA sequencing) data. | bioMate-AI/ | 804 | — | ~4.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 6 | BEER implements a Bayesian model for analyzing phage-immunoprecipitation sequencing (PhIP-seq) data. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 7 | Precise knowledge on the binding sites of an RNA-binding protein (RBP) is key to understand (post-) transcriptional regulatory processes. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 8 | In recent years a wealth of biological data has become available in public data repositories. | bioMate-AI/ | 804 | — | ~4.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 9 | the R package BioNAR, developed to step by step analysis of PPI network. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 10 | The BloodGen3Module package provides functions for R user performing module repertoire analyses and generating fingerprint representations. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 11 | BUSseq R package fits an interpretable Bayesian hierarchical model---the Batch Effects Correction with Unknown Subtypes for scRNA seq Data (BUSseq)---to correct batch effects in the presence of… | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 12 | This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 13 | Methods to infer clonal tree configuration for a population of cells using single-cell RNA-seq data (scRNA-seq), and possibly other data modalities. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 14 | This package provides the visualization of bayesian network inferred from gene expression data. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 15 | The package CellBarcode performs Cellular DNA Barcode analysis. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 16 | The cellxgene data portal (https://cellxgene.cziscience.com/) provides a graphical user interface to collections of single-cell sequence data processed in standard ways to 'count matrix' summaries. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 17 | ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. | bioMate-AI/ | 804 | — | ~3.8k | Automated safety check: Pass | Unknown | 3 mo ago |
| 18 | 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. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 19 | This package encapsulate many functions to conduct a differential topology analysis. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 20 | Statistical and computational method to analyze the co-expression of gene pairs at single cell level. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 21 | Provides S4 classes for general nucleases, CRISPR nucleases, CRISPR nickases, and base editors.Several CRISPR-specific genome arithmetic functions are implemented to help extract genomic coordinates… | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 22 | Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 23 | Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs). | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 24 | Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 25 | MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 26 | This R package supports interactive visualization of multi-channel images and segmentation masks generated by imaging mass cytometry and other highly multiplexed imaging techniques using shiny. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 27 | This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 28 | A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 29 | Uses DESeq2 to estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. | bioMate-AI/ | 804 | — | ~4.8k | Automated safety check: Pass | Unknown | 3 mo ago |
| 30 | Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 31 | performing all the steps of gene expression meta-analysis considering the possible existence of missing genes. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 32 | Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 33 | doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication. | bioMate-AI/ | 804 | — | ~914 | Automated safety check: Pass | Unknown | 3 mo ago |
| 34 | The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. | bioMate-AI/ | 804 | — | ~4.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 35 | Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 36 | This package provides a workflow for the use of EaSIeR tool, developed to assess patients' likelihood to respond to ICB therapies providing just the patients' RNA-seq data as input. | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 37 | Estimates differential gene expression for short read sequence count using methods appropriate for count data. | bioMate-AI/ | 804 | — | ~3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 38 | Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 39 | epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 40 | The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq, DNA methyation or genomic conservation data) centered at… | bioMate-AI/ | 804 | — | ~2.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 41 | The creation of effective visualizations is a fundamental component of data analysis. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 42 | This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 43 | The FDA Adverse Event Reporting System (FAERS) is a database used for the spontaneous reporting of adverse events and medication errors related to human drugs and therapeutic biological products. | bioMate-AI/ | 804 | — | ~822 | Automated safety check: Pass | Unknown | 3 mo ago |
| 44 | This package implements functions to find influential TF and target based on different input type. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 45 | This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 46 | This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 47 | The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. | bioMate-AI/ | 804 | — | ~4.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 48 | Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA) provide us with a wealth of data, such as RNA-seq, DNA Methylation, SNP and Copy number variation data. | bioMate-AI/ | 804 | — | ~2.2k | Automated safety check: Pass | Unknown | 3 mo ago |
Questions, answered from the data.
What is the best skill by bioMate-AI?
Bioconductor Annotationhub from bioMate-AI/biomate-bioconductor-kb ranks first of the 112 skills by bioMate-AI listed here, with the highest score: its repository has 804 GitHub stars, its SKILL.md loads about 2.9k tokens and it passes the automated safety check with no findings. Next come Bioconductor Asurat and Bioconductor Awst.
Are bioMate-AI's skills official?
None yet. All 112 skills by bioMate-AI listed here come from community repositories; a skill counts as official when the product's own GitHub organization publishes it.
How are these skills ranked?
By Skill Navigator score, which combines the GitHub stars of the skill's repository (shared across that repo's skills and discounted for large collections), how many other GitHub owners carry a copy of the skill, and automated SKILL.md quality checks, minus penalties for safety-check warnings and for each further skill from the same repository. Skills that fail the safety check are not listed.