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By bioMate-AI
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| # | 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 |
