biomate-ai
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- ▌ Bioconductor Limma · biomate-aiGiven a matrix of counts (e.g. from featureCounts) and optional information about the genes, this tool performs differential expression (DE) using the limma Bioconductor package and produces plots and tables useful in DE analysis. Interacti
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- ▌ Bioconductor Scran · biomate-aiImplements miscellaneous functions for interpretation of single-cell RNA-seq data. Methods are provided for assignment of cell cycle phase, detection of highly variable and significantly correlated genes, identification of marker genes, and
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- ▌ Bioconductor Chipseeker · biomate-aiChIPseeker is a Bioconductor package for annotating ChIP-seq data analysis. Peak Annotation is performed by the annotatePeak function. The position and strand information of nearest genes are reported, in addition to the distance from the p
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- ▌ Bioconductor Residualmatrix · biomate-aiProvides delayed computation of a matrix of residuals after fitting a linear model to each column of an input matrix. Also supports partial computation of residuals where selected factors are to be preserved in the output matrix. Implements
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- ▌ Bioconductor Genomicranges · biomate-aiThe 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. NGS data). The GenomicRanges package defines general purpose
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- ▌ Bioconductor Mscoreutils · biomate-aiMsCoreUtils defines low-level functions for mass spectrometry data and is independent of any high-level data structures. These functions include mass spectra processing functions (noise estimation, smoothing, binning, baseline estimation),
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- ▌ Bioconductor Apeglm · biomate-aiapeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.
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- ▌ Bioconductor Aucell · biomate-aiAUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched with
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- ▌ Bioconductor Deseq2 · biomate-aiUses 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.
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- ▌ Bioconductor Scater · biomate-aiA collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.
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- ▌ Bioconductor Treeio · biomate-ai'treeio' is an R package to make it easier to import and store phylogenetic tree with associated data; and to link external data from different sources to phylogeny. It also supports exporting phylogenetic tree with heterogeneous associated
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- ▌ Bioconductor Complexheatmap · biomate-aiComplex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential patterns. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports various
- ▌ Bioconductor Biomformat · biomate-aiThis is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limi
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- ▌ Bioconductor Metapod · biomate-aiImplements a variety of methods for combining p-values in differential analyses of genome-scale datasets. Functions can combine p-values across different tests in the same analysis (e.g., genomic windows in ChIP-seq, exons in RNA-seq) or fo
- ▌ Bioconductor Monocle · biomate-aiMonocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progre
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- ▌ Bioconductor Scuttle · biomate-aiProvides basic utility functions for performing single-cell analyses, focusing on simple normalization, quality control and data transformations. Also provides some helper functions to assist development of other packages.
- ▌ Bioconductor Singler · biomate-aiPerforms unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
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- ▌ Bioconductor Clusterprofiler · biomate-aiThis package supports functional characteristics of both coding and non-coding genomics data for thousands of species with up-to-date gene annotation. It provides a univeral interface for gene functional annotation from a variety of sources
- ▌ Bioconductor Genomicfeatures · biomate-aiExtract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a
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- ▌ Bioconductor Geoquery · biomate-aiThis tool fetches microarray data directly from GEO database, based on the GEOQuery R package. Given a GSE accession ID, it returns an Rdata object containing the data and a text file (.cond file) summarizing the conditions of the experimen
- ▌ Bioconductor Gseabase · biomate-aiThis package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).
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- ▌ Bioconductor Pathview · biomate-aiPathview is a stand-alone software package for pathway based data integration and visualization.
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- ▌ Bioconductor Siggenes · biomate-aiIdentification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).
- ▌ Bioconductor Tximport · biomate-aiCurrent version only works in 'merge' mode: A single table of gene summarizations is generated with one column for each sample file.
- ▌ Bioconductor Snpstats · biomate-aiClasses and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.
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- ▌ Bioconductor Zellkonverter · biomate-aiProvides methods to convert between Python AnnData objects and SingleCellExperiment objects. These are primarily intended for use by downstream Bioconductor packages that wrap Python methods for single-cell data analysis. It also includes f
- ▌ Bioconductor Batchelor · biomate-aiImplements a variety of methods for batch correction of single-cell (RNA sequencing) data. This includes methods based on detecting mutually nearest neighbors, as well as several efficient variants of linear regression of the log-expression
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- ▌ Bioconductor Glmgampoi · biomate-aiFit linear models to overdispersed count data. The package can estimate the overdispersion and fit repeated models for matrix input. It is designed to handle large input datasets as they typically occur in single cell RNA-seq experiments.
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- ▌ Bioconductor Genomicalignments · biomate-aiProvides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working wit
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- ▌ Bioconductor Illuminaio · biomate-aiTools for parsing Illumina's microarray output files, including IDAT.
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- ▌ Bioconductor Scdblfinder · biomate-aiThe scDblFinder package gathers various methods for the detection and handling of doublets/multiplets in single-cell sequencing data (i.e. multiple cells captured within the same droplet or reaction volume). It includes methods formerly fou
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- ▌ Bioconductor Multiassayexperiment · biomate-aiHarmonize data management of multiple experimental assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of st
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- ▌ Bioconductor Dropletutils · biomate-aiThe filtering uses intelligent methods to generate output 10X matrices as would be otherwise generated by CellRanger. The ranking option serves to illustrate the number of detected barcodes in the sample.
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- ▌ Bioconductor Consensusclusterplus · biomate-aialgorithm for determining cluster count and membership by stability evidence in unsupervised analysis
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- ▌ Bioconductor Annotationhub · biomate-aiThis package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, En
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