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Research & Science · By bioMate-AI
Skills
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| # | Skill | Repository | Stars | Used in | Tokens | Auto-check | Licence | Updated |
|---|---|---|---|---|---|---|---|---|
| 49 | 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 |
| 50 | 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 |
| 51 | 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 |
| 52 | 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 |
| 53 | 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 |
| 54 | 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 |
| 55 | 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 |
| 56 | 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 |
| 57 | 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 |
| 58 | 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 |
| 59 | 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 |
| 60 | Tools to analyze & visualize Illumina Infinium methylation arrays. | bioMate-AI/ | 804 | — | ~4.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 61 | 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 |
| 62 | 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 |
| 63 | 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 |
| 64 | 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 |
| 65 | 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 |
| 66 | 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 |
| 67 | Save MultiAssayExperiments to h5mu files supported by muon and mudata. | bioMate-AI/ | 804 | — | ~1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 68 | 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 |
| 69 | omicsViewer visualizes ExpressionSet (or SummarizedExperiment) in an interactive way. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 70 | 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 |
| 71 | 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 |
| 72 | 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 |
| 73 | 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 |
| 74 | This package performs differential pattern analysis for Ribo-seq data. | bioMate-AI/ | 804 | — | ~1.8k | Automated safety check: Pass | Unknown | 3 mo ago |
| 75 | 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 |
| 76 | 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 |
| 77 | 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 |
| 78 | 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 |
| 79 | 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 |
| 80 | 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 |
| 81 | Implements miscellaneous functions for interpretation of single-cell RNA-seq data. | bioMate-AI/ | 804 | — | ~4.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 82 | 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/ | 804 | — | ~818 | Automated safety check: Pass | Unknown | 3 mo ago |
| 83 | sechm provides a simple interface between SummarizedExperiment objects and the ComplexHeatmap package. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 84 | SGC is a semi-supervised pipeline for gene clustering in gene co-expression networks. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 85 | SimBu can be used to simulate bulk RNA-seq datasets with known cell type fractions. | bioMate-AI/ | 804 | — | ~1.4k | Automated safety check: Pass | Unknown | 3 mo ago |
| 86 | Image segmentation is the process of identifying the borders of individual objects (in this case cells) within an image. | bioMate-AI/ | 804 | — | ~1.2k | Automated safety check: Pass | Unknown | 3 mo ago |
| 87 | Defines a S4 class for storing data from single-cell experiments. | bioMate-AI/ | 804 | — | ~4.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 88 | SpatialDE is a method to find spatially variable genes (SVG) from spatial transcriptomics data. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 89 | The analysis and visualization of alternative splicing (AS) events from RNA sequencing data remains challenging. | bioMate-AI/ | 804 | — | ~2.1k | Automated safety check: Pass | Unknown | 3 mo ago |
| 90 | SpotClean is a computational method to adjust for spot swapping in spatial transcriptomics data. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 91 | 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/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 92 | standR is an user-friendly R package providing functions to assist conducting good-practice analysis of Nanostring's GeoMX DSP data. | bioMate-AI/ | 804 | — | ~1.3k | Automated safety check: Pass | Unknown | 3 mo ago |
| 93 | Statial is a suite of functions for identifying changes in cell state. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 94 | Generate SuperSigs (supervised mutational signatures) from single nucleotide variants in the cancer genome. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 95 | syntenet can be used to infer synteny networks from whole-genome protein sequences and analyze them. | bioMate-AI/ | 804 | — | ~1.5k | Automated safety check: Pass | Unknown | 3 mo ago |
| 96 | Offers functions for plotting split (or implicit) networks (unrooted, undirected) and explicit networks (rooted, directed) with reticulations extending. | bioMate-AI/ | 804 | — | ~1.1k | Automated safety check: Pass | Unknown | 3 mo ago |
