Best agent skills for researchers, page 134

This package encapsulate many functions to conduct a differential topology analysis.

bioMate-AI/biomate-bioconductor-kb

Statistical and computational method to analyze the co-expression of gene pairs at single cell level.

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…

bioMate-AI/biomate-bioconductor-kb

Provides a comprehensive suite of functions to design and annotate CRISPR guide RNA (gRNAs) sequences.

bioMate-AI/biomate-bioconductor-kb

Provides R wrappers of several on-target and off-target scoring methods for CRISPR guide RNAs (gRNAs).

bioMate-AI/biomate-bioconductor-kb

Provides functionalities to visualize and contextualize CRISPR guide RNAs (gRNAs) on genomic tracks across nucleases and applications.

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.

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.

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.

bioMate-AI/biomate-bioconductor-kb

A package for demultiplexing single-cell sequencing experiments of pooled cells labeled with barcode oligonucleotides.

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.

bioMate-AI/biomate-bioconductor-kb

Intuitive framework for identifying spatially variable genes (SVGs) via edgeR, a popular method for performing differential expression analyses.

bioMate-AI/biomate-bioconductor-kb

performing all the steps of gene expression meta-analysis considering the possible existence of missing genes.

bioMate-AI/biomate-bioconductor-kb

Dino normalizes single-cell, mRNA sequencing data to correct for technical variation, particularly sequencing depth, prior to downstream analysis.

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.

bioMate-AI/biomate-bioconductor-kb

The filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger.

bioMate-AI/biomate-bioconductor-kb

Provides utilities for identifying drug-target interactions for sets of small molecule or gene/protein identifiers.

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.

bioMate-AI/biomate-bioconductor-kb

Estimates differential gene expression for short read sequence count using methods appropriate for count data.

bioMate-AI/biomate-bioconductor-kb

Epialleles are specific DNA methylation patterns that are mitotically and/or meiotically inherited.

bioMate-AI/biomate-bioconductor-kb

epigraHMM provides a set of tools for the analysis of epigenomic data based on hidden Markov Models.

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…

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.

bioMate-AI/biomate-bioconductor-kb

This package implements functions to find influential TF and target based on different input type.

bioMate-AI/biomate-bioconductor-kb

This package implements a metabolic network analysis pipeline to identify an active metabolic module based on high throughput data.

bioMate-AI/biomate-bioconductor-kb

This package contain functions to run genomic instability analysis (GIA) from scRNA-Seq data.

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.

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.

bioMate-AI/biomate-bioconductor-kb

Manhattan plot and QQ Plot are commonly used to visualize the end result of Genome Wide Association Study.

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.

bioMate-AI/biomate-bioconductor-kb

Systematic 3D interaction calls and differential analysis for Hi-C and HiChIP.

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.

bioMate-AI/biomate-bioconductor-kb

HiContacts provides a collection of tools to analyse and visualize Hi-C datasets imported in R by HiCExperiment.

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.

bioMate-AI/biomate-bioconductor-kb

MHC (major histocompatibility complex) molecules are cell surface complexes that present antigens to T cells.

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.

bioMate-AI/biomate-bioconductor-kb

Given a matrix of counts (e.g. An agent skill from bioMate-AI/biomate-bioconductor-kb.

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.

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.

bioMate-AI/biomate-bioconductor-kb

The Model-based Analysis of ChIP-Seq (MACS) is a widely used toolkit for identifying transcript factor binding sites.

bioMate-AI/biomate-bioconductor-kb

mastR is an R package designed for automated screening of signatures of interest for specific research questions.

bioMate-AI/biomate-bioconductor-kb

Tools to analyze & visualize Illumina Infinium methylation arrays.

bioMate-AI/biomate-bioconductor-kb

mirTarRnaSeq R package can be used for interactive mRNA miRNA sequencing statistical analysis.

bioMate-AI/biomate-bioconductor-kb

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/biomate-bioconductor-kb

Mass spectrometry (MS) data backend supporting import and export of MS/MS library spectra from MassBank record files.

bioMate-AI/biomate-bioconductor-kb

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/biomate-bioconductor-kb

MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.

bioMate-AI/biomate-bioconductor-kb

Tools for LiP peptide and protein significance analysis. An agent skill from bioMate-AI/biomate-bioconductor-kb.

bioMate-AI/biomate-bioconductor-kb