#98255Bioconductor Cellbarcode
bioMate-AI/biomate-bioconductor-kb
The package CellBarcode performs Cellular DNA Barcode analysis.
98,398 skills
All agent skills page 2020 of 2050
Open-source SKILL.md skills for Claude Code, Codex, Cursor, Gemini CLI, GitHub Copilot and other agents, ranked by GitHub stars, adoption and SKILL.md quality. Skills that fail our automated safety check are left out.
#98256Bioconductor Cellxgenedp
bioMate-AI/biomate-bioconductor-kb
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.
#98257Bioconductor Chipseeker
bioMate-AI/biomate-bioconductor-kb
ChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis.
#98258Bioconductor Cogeqc
bioMate-AI/biomate-bioconductor-kb
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.
#98259Bioconductor Condiments
bioMate-AI/biomate-bioconductor-kb
This package encapsulate many functions to conduct a differential topology analysis.
#98260Bioconductor Cotan
bioMate-AI/biomate-bioconductor-kb
Statistical and computational method to analyze the co-expression of gene pairs at single cell level.
#98261Bioconductor Crisprbase
bioMate-AI/biomate-bioconductor-kb
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…
#98262Bioconductor Crisprdesign
bioMate-AI/biomate-bioconductor-kb
Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences.
#98263Bioconductor Crisprscore
bioMate-AI/biomate-bioconductor-kb
Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs).
#98264Bioconductor Crisprviz
bioMate-AI/biomate-bioconductor-kb
Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications.
#98265Bioconductor Cytomem
bioMate-AI/biomate-bioconductor-kb
MEM, Marker Enrichment Modeling, automatically generates and displays quantitative labels for cell populations that have been identified from single-cell data.
#98266Bioconductor Cytoviewer
bioMate-AI/biomate-bioconductor-kb
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.
#98267Bioconductor Deconvr
bioMate-AI/biomate-bioconductor-kb
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.
#98268Bioconductor Demuxmix
bioMate-AI/biomate-bioconductor-kb
A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides.
#98269Bioconductor Deseq2
bioMate-AI/biomate-bioconductor-kb
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.
#98270Bioconductor Despace
bioMate-AI/biomate-bioconductor-kb
Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses.
#98271Bioconductor Dexma
bioMate-AI/biomate-bioconductor-kb
performing all the steps of gene expression meta-analysis considering the possible existence of missing genes.
#98272Bioconductor Dino
bioMate-AI/biomate-bioconductor-kb
Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis.
#98273Bioconductor Doubletrouble
bioMate-AI/biomate-bioconductor-kb
doubletrouble aims to identify duplicated genes from whole-genome protein sequences and classify them based on their modes of duplication.
#98274Bioconductor Dropletutils
bioMate-AI/biomate-bioconductor-kb
The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger.
#98275Bioconductor Drugtargetinteractions
bioMate-AI/biomate-bioconductor-kb
Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers.
#98276Bioconductor Easier
bioMate-AI/biomate-bioconductor-kb
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.
#98277Bioconductor Edger
bioMate-AI/biomate-bioconductor-kb
Estimates differential gene expression for short read sequence count using methods appropriate for count data.
#98278Bioconductor Epialleler
bioMate-AI/biomate-bioconductor-kb
Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited.
#98279Bioconductor Epigrahmm
bioMate-AI/biomate-bioconductor-kb
epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.
#98280Bioconductor Epistack
bioMate-AI/biomate-bioconductor-kb
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…
#98281Bioconductor Escher
bioMate-AI/biomate-bioconductor-kb
The creation of effective visualizations is a fundamental component of data analysis.
#98282Bioconductor Extrachips
bioMate-AI/biomate-bioconductor-kb
This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data.
#98283Bioconductor Faers
bioMate-AI/biomate-bioconductor-kb
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.
#98284Bioconductor Findit2
bioMate-AI/biomate-bioconductor-kb
This package implements functions to find influential TF and target based on different input type.
#98285Bioconductor Gatom
bioMate-AI/biomate-bioconductor-kb
This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data.
#98286Bioconductor Genomicinstability
bioMate-AI/biomate-bioconductor-kb
This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data.
#98287Bioconductor Genomicranges
bioMate-AI/biomate-bioconductor-kb
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.
#98288Bioconductor Geotcgadata
bioMate-AI/biomate-bioconductor-kb
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.
#98289Bioconductor Ggmanh
bioMate-AI/biomate-bioconductor-kb
Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study.
#98290Bioconductor Granulator
bioMate-AI/biomate-bioconductor-kb
granulator is an R package for the cell type deconvolution of heterogeneous tissues based on bulk RNA-seq data or single cell RNA-seq expression profiles.
#98291Bioconductor Harmonizr
bioMate-AI/biomate-bioconductor-kb
An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma.
#98292Bioconductor Hicdcplus
bioMate-AI/biomate-bioconductor-kb
Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.
#98293Bioconductor Hicexperiment
bioMate-AI/biomate-bioconductor-kb
R generic interface to Hi-C contact matrices in .(m)cool, .hic or HiC-Pro derived formats, as well as other Hi-C processed file formats.
#98294Bioconductor Hicontacts
bioMate-AI/biomate-bioconductor-kb
HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.
#98295Bioconductor Hoodscanr
bioMate-AI/biomate-bioconductor-kb
hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution.
#98296Bioconductor Immunotation
bioMate-AI/biomate-bioconductor-kb
MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells.
#98297Bioconductor Intercellar
bioMate-AI/biomate-bioconductor-kb
InterCellar is implemented as an R/Bioconductor Package containing a Shiny app that allows users to interactively analyze cell-cell communication from scRNA-seq data.
#98298Bioconductor Limma
bioMate-AI/biomate-bioconductor-kb
Given a matrix of counts (e.g. An agent skill from bioMate-AI/biomate-bioconductor-kb.
#98299Bioconductor Lintind
bioMate-AI/biomate-bioconductor-kb
When we combine gene-editing technology and sequencing technology, we need to reconstruct a lineage tree from alleles generated and calculate the similarity between each pair of groups.
#98300Bioconductor Lisaclust
bioMate-AI/biomate-bioconductor-kb
lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar.
#98301Bioconductor Macsr
bioMate-AI/biomate-bioconductor-kb
The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites.
#98302Bioconductor Mastr
bioMate-AI/biomate-bioconductor-kb
mastR is an R package designed for automated screening of signatures of interest for specific research questions.