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r-pamr
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public |
Some functions for sample classification in microarrays
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2025-04-22 |
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ngless
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public |
A tool for short-read processing with a focus on metagenomics
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2025-04-22 |
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r-ic10trainingdata
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public |
Training datasets for iC10; which implements the classifier described in the paper 'Genome-driven integrated classification of breast cancer validated in over 7,500 samples' (Ali HR et al., Genome Biology 2014). It uses copy number and/or expression form breast cancer data, trains a pamr classifier (Tibshirani et al.) with the features available and predicts the iC10 group. Genomic annotation for the training dataset has been obtained from Mark Dunning's lluminaHumanv3.db package.
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2025-04-22 |
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bioconductor-banocc
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public |
Bayesian ANalysis Of Compositional Covariance
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2025-04-22 |
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r-swamp
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public |
Collection of functions to connect the structure of the data with the information on the samples. Three types of associations are covered: 1. linear model of principal components. 2. hierarchical clustering analysis. 3. distribution of features-sample annotation associations. Additionally, the inter-relation between sample annotations can be analyzed. Simple methods are provided for the correction of batch effects and removal of principal components.
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2025-04-22 |
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mummer4
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public |
MUMmer is a system for rapidly aligning entire genomes.
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2025-04-22 |
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secimtools
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public |
Metabolomics tools from the SECIM project
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2025-04-22 |
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r-precrec
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public |
Accurate calculations and visualization of precision-recall and ROC (Receiver Operator Characteristics) curves.
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2025-04-22 |
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bioconductor-phosphonormalizer
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public |
Compensates for the bias introduced by median normalization in
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2025-04-22 |
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bioconductor-ndexr
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public |
NDEx R client library
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2025-04-22 |
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bioconductor-multiomicsviz
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public |
Plot the effect of one omics data on other omics data along the chromosome
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2025-04-22 |
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strudel
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public |
Strudel is a graphical tool for visualizing genetic and physical maps of genomes for comparative purposes.
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2025-04-22 |
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bioconductor-jaspar2018
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public |
Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).
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2025-04-22 |
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dx-cwl
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public |
Import and run CWL workflows on DNAnexus
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2025-04-22 |
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bioconductor-genomicdatacommons
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public |
NIH / NCI Genomic Data Commons Access
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2025-04-22 |
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bioconductor-ppinfer
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public |
Inferring functionally related proteins using protein interaction networks
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2025-04-22 |
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bioconductor-heatmaps
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public |
Flexible Heatmaps for Functional Genomics and Sequence Features
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2025-04-22 |
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bioconductor-atacseqqc
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public |
ATAC-seq Quality Control
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2025-04-22 |
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bioconductor-yeastexpdata
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public |
Yeast Experimental Data
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2025-04-22 |
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bioconductor-chippeakanno
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public |
Batch annotation of the peaks identified from either ChIP-seq, ChIP-chip experiments, or any experiments that result in large number of genomic interval data
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2025-04-22 |
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bioconductor-genomicscores
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public |
Infrastructure to work with genomewide position-specific scores
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2025-04-22 |
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ndex-python
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public |
NDEx Python includes a client and a data model.
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2025-04-22 |
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bioconductor-codex
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public |
A Normalization and Copy Number Variation Detection Method for Whole Exome Sequencing
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2025-04-22 |
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r-genabel
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public |
A package for genome-wide association analysis between quantitative or binary traits and single-nucleotide polymorphisms (SNPs).
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2025-04-22 |
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hicbrowser
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public |
A simple web browser to visualize Hi-C and other genomic tracks (bigwig, bed, interactions).
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2025-04-22 |
