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bioconductor-spatialfeatureexperiment
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public |
Integrating SpatialExperiment with Simple Features in sf
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2025-04-22 |
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bioconductor-mobilitytransformr
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public |
Effective mobility scale transformation of CE-MS(/MS) data
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2025-04-22 |
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bioconductor-fusesom
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public |
A Correlation Based Multiview Self Organizing Maps Clustering For IMC Datasets
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2025-04-22 |
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bioconductor-scddboost
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public |
A compositional model to assess expression changes from single-cell rna-seq data
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2025-04-22 |
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bioconductor-spasim
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public |
Spatial point data simulator for tissue images
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2025-04-22 |
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bioconductor-beer
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public |
Bayesian Enrichment Estimation in R
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2025-04-22 |
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bioconductor-qmtools
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public |
Quantitative Metabolomics Data Processing Tools
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2025-04-22 |
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bioconductor-cnvmetrics
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public |
Copy Number Variant Metrics
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2025-04-22 |
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bioconductor-ggmanh
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public |
Visualization Tool for GWAS Result
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2025-04-22 |
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r-rspectral
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public |
Implements the network clustering algorithm described in Newman (2006) <doi:10.1103/PhysRevE.74.036104>. The complete iterative algorithm comprises of two steps. In the first step, the network is expressed in terms of its leading eigenvalue and eigenvector and recursively partition into two communities. Partitioning occurs if the maximum positive eigenvalue is greater than the tolerance (10e-5) for the current partition, and if it results in a positive contribution to the Modularity. Given an initial separation using the leading eigen step, 'rSpectral' then continues to maximise for the change in Modularity using a fine-tuning step - or variate thereof. The first stage here is to find the node which, when moved from one community to another, gives the maximum change in Modularity. This node’s community is then fixed and we repeat the process until all nodes have been moved. The whole process is repeated from this new state until the change in the Modularity, between the new and old state, is less than the predefined tolerance. A slight variant of the fine-tuning step, which can improve speed of the calculation, is also provided. Instead of moving each node into each community in turn, we only consider moves of neighbouring nodes, found in different communities, to the community of the current node of interest. The two steps process is repeatedly applied to each new community found, subdivided each community into two new communities, until we are unable to find any division that results in a positive change in Modularity.
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2025-04-22 |
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bioconductor-rolde
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public |
RolDE: Robust longitudinal Differential Expression
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2025-04-22 |
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bioconductor-compounddb
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public |
Creating and Using (Chemical) Compound Annotation Databases
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2025-04-22 |
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bioconductor-cellxgenedp
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public |
Discover and Access Single Cell Data Sets in the CELLxGENE Data Portal
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2025-04-22 |
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bioconductor-redisparam
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public |
Provide a 'redis' back-end for BiocParallel
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2025-04-22 |
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bioconductor-oncoscanr
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public |
Secondary analyses of CNV data (HRD and more)
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2025-04-22 |
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freddie
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public |
Annotation-independent detection of splicing isoforms using RNA long-reads
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2025-04-22 |
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bioconductor-biodbexpasy
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public |
biodbExpasy, a library for connecting to Expasy ENZYME database.
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2025-04-22 |
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bioconductor-biodbmirbase
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public |
biodbMirbase, a library for connecting to miRBase mature database
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2025-04-22 |
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bioconductor-biodbncbi
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public |
biodbNcbi, a library for connecting to NCBI Databases.
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2025-04-22 |
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massiveqc
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public |
Tools for QC massive RNA-seq samples
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2025-04-22 |
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bioconductor-cytomem
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public |
Marker Enrichment Modeling (MEM)
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2025-04-22 |
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haptools
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public |
Ancestry and haplotype aware simulation of genotypes and phenotypes for complex trait analysis
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2025-04-22 |
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bioconductor-stdeconvolve
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public |
Reference-free Cell-Type Deconvolution of Multi-Cellular Spatially Resolved Transcriptomics Data
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2025-04-22 |
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bioconductor-msbackendmsp
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public |
Mass Spectrometry Data Backend for NIST msp Files
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2025-04-22 |
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bioconductor-updateobject
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public |
Find/fix old serialized S4 instances
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2025-04-22 |
