Category
Best research and science skills, page 124
Research & Science skills, ranked
Ranked by score. Sort bymost stars,trending,newest,recently updated
| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 5905 | 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 |
| 5906 | 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 |
| 5907 | 5907.Bioconductor Easier 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 |
| 5908 | 5908.Bioconductor Edger 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 |
| 5909 | 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 |
| 5910 | 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 |
| 5911 | 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 |
| 5912 | 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 |
| 5913 | 5913.Bioconductor Findit2 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 |
| 5914 | 5914.Bioconductor Gatom 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 |
| 5915 | 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 |
| 5916 | 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 |
| 5917 | 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 |
| 5918 | 5918.Bioconductor Ggmanh Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5919 | 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. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5920 | An implementation, which takes input data and makes it available for proper batch effect removal by ComBat or Limma. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5921 | Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5922 | 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. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5923 | HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5924 | hoodscanR is an user-friendly R package providing functions to assist cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5925 | MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5926 | 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. | bioMate-AI/ | 804 | — | ~985 | Automated safety check: Pass | Unknown | 3 mo ago |
| 5927 | 5927.Bioconductor Limma Given a matrix of counts (e.g. An agent skill from bioMate-AI/biomate-bioconductor-kb. | bioMate-AI/ | 804 | — | ~2.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5928 | 5928.Bioconductor Lintind 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. | bioMate-AI/ | 804 | — | ~1.7k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5929 | lisaClust provides a series of functions to identify and visualise regions of tissue where spatial associations between cell-types is similar. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5930 | 5930.Bioconductor Macsr The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites. | bioMate-AI/ | 804 | — | ~890 | Automated safety check: Pass | Unknown | 3 mo ago |
| 5931 | 5931.Bioconductor Mastr mastR is an R package designed for automated screening of signatures of interest for specific research questions. | bioMate-AI/ | 804 | — | ~1.6k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5932 | 5932.Bioconductor Minfi Tools to analyze & visualize Illumina Infinium methylation arrays. | bioMate-AI/ | 804 | — | ~4.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5933 | mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis. | bioMate-AI/ | 804 | — | ~2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5934 | MSA2dist calculates pairwise distances between all sequences of a DNAStringSet or a AAStringSet using a custom score matrix and conducts codon based analysis. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5935 | Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5936 | The MsDataHub package uses the ExperimentHub infrastructure to distribute raw mass spectrometry data files, peptide spectrum matches or quantitative data from proteomics and metabolomics experiments. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5937 | 5937.Bioconductor Msnbase MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. | bioMate-AI/ | 804 | — | ~3.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5938 | Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5939 | 5939.Bioconductor Mudata Save MultiAssayExperiments to h5mu files supported by muon and mudata. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5940 | 5940.Bioconductor Nnsvg Method for scalable identification of spatially variable genes (SVGs) in spatially-resolved transcriptomics data. | bioMate-AI/ | 804 | — | ~925 | Automated safety check: Pass | Unknown | 3 mo ago |
| 5941 | omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5942 | 5942.Bioconductor Ompbam This packages provides C++ header files for developers wishing to create R packages that processes BAM files. | bioMate-AI/ | 804 | — | ~993 | Automated safety check: Pass | Unknown | 3 mo ago |
| 5943 | The ORFhunteR package is a R and C++ library for an automatic determination and annotation of open reading frames (ORF) in a large set of RNA molecules. | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5944 | PhIPData defines an S4 class for phage-immunoprecipitation sequencing (PhIP-seq) experiments. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5945 | 5945.Bioconductor Rblast Seamlessly interfaces the Basic Local Alignment Search Tool (BLAST) to search genetic sequence data bases. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5946 | This package performs differential pattern analysis for Ribo-seq data. | bioMate-AI/ | 804 | — | ~1.8k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5947 | 5947.Bioconductor Scanmir A set of tools for working with miRNA affinity models (KdModels), efficiently scanning for miRNA binding sites, and predicting target repression. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5948 | The package comprises a set of pretrained machine learning models to predict basic immune cell types. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5949 | 5949.Bioconductor Scarray Provides large-scale single-cell omics data manipulation using Genomic Data Structure (GDS) files. | bioMate-AI/ | 804 | — | ~968 | Automated safety check: Pass | Unknown | 3 mo ago |
| 5950 | 5950.Bioconductor Scater 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/ | 804 | — | ~4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5951 | 5951.Bioconductor Sccomp A robust and outlier-aware method for testing differential tissue composition from single-cell data. | bioMate-AI/ | 804 | — | ~1.9k | Automated safety check: Pass | Unknown | 3 mo ago |
| 5952 | 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/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
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