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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2024-12-14 |
r-ic10
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public |
Implementation of 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.
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2024-12-14 |
cpat
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public |
Coding Potential Assessment Tool
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2024-12-14 |
bioconductor-beaddatapackr
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public |
Compression of Illumina BeadArray data
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2024-12-14 |
metaphyler
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public |
No Summary
|
2024-12-14 |
trumicount
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public |
For NGS experiments using unique molecular identifiers (UMIs), molecules that are lost entirely during sequencing cause under- estimation of the molecule count, and amplification artifacts like PCR chimeras cause over-estimation. TRUmiCount corrects UMI data for both types of errors, thus improving the accuracy of measured molecule counts considerably.
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2024-12-14 |
perl-class-methodmaker
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public |
Create generic methods for OO Perl
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2024-12-14 |
mykatlas
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public |
Assists in discoveries of antibiotic-resistance with mykrobe
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2024-12-14 |
das_tool
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public |
Recovery of genomes from metagenomes via a dereplication,
aggregation and scoring strategy.
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2024-12-14 |
bioconductor-biocworkflowtools
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public |
Tools to aid the development of Bioconductor Workflow packages
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2024-12-14 |
bioconductor-illuminaio
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public |
Parsing Illumina Microarray Output Files
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2024-12-14 |
bioconductor-process
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public |
Ciphergen SELDI-TOF Processing
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2024-12-14 |
bioconductor-harman
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public |
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
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2024-12-14 |
perl-json-create
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public |
fast, minimal, UTF-8-only serialization of data to JSON
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2024-12-14 |
perl-extutils-cppguess
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public |
guess C++ compiler and flags
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2024-12-14 |
infernal
|
public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
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2024-12-14 |
r-facets
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public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
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2024-12-14 |
fermi2
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public |
Fermi2 focuses on the exploration of FMD-index as a graph.
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2024-12-14 |
ucsc-websync
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public |
download from https server, using files.txt on their end to get the list of files
|
2024-12-14 |
perl-devel-size
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public |
Perl extension for finding the memory usage of Perl variables
|
2024-12-14 |
bioconductor-unifiedwmwqpcr
|
public |
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
|
2024-12-14 |
ucsc-chopfalines
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public |
Read in FA file with long lines and rewrite it with shorter lines
|
2024-12-14 |
bioconductor-parody
|
public |
Parametric And Resistant Outlier DYtection
|
2024-12-14 |
bioconductor-rgsea
|
public |
Random Gene Set Enrichment Analysis
|
2024-12-14 |
bioconductor-rrho
|
public |
Inference on agreement between ordered lists
|
2024-12-14 |
pepnovo
|
public |
No Summary
|
2024-12-14 |
bioconductor-mvcclass
|
public |
Model-View-Controller (MVC) Classes
|
2024-12-14 |
bioconductor-sights
|
public |
Statistics and dIagnostic Graphs for HTS
|
2024-12-14 |
bioconductor-phosphonormalizer
|
public |
Compensates for the bias introduced by median normalization in
|
2024-12-14 |
bioconductor-ggtree
|
public |
an R package for visualization of tree and annotation data
|
2024-12-14 |
bioconductor-preprocesscore
|
public |
A collection of pre-processing functions
|
2024-12-14 |
bioconductor-diffgeneanalysis
|
public |
Performs differential gene expression Analysis
|
2024-12-14 |
bioconductor-diffustats
|
public |
Diffusion scores on biological networks
|
2024-12-14 |
bioconductor-clst
|
public |
Classification by local similarity threshold
|
2024-12-14 |
bioconductor-inpower
|
public |
An R package for computing the number of susceptibility SNPs
|
2024-12-14 |
bioconductor-ctc
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public |
Cluster and Tree Conversion.
|
2024-12-14 |
bioconductor-isolde
|
public |
Integrative Statistics of alleLe Dependent Expression
|
2024-12-14 |
bioconductor-rcaspar
|
public |
A package for survival time prediction based on a piecewise baseline hazard Cox regression model.
|
2024-12-14 |
bioconductor-cqn
|
public |
Conditional quantile normalization
|
2024-12-14 |
bioconductor-epivizrserver
|
public |
WebSocket server infrastructure for epivizr apps and packages
|
2024-12-14 |
ucsc-pslsomerecords
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public |
Extract multiple psl records
|
2024-12-14 |
bioconductor-antiprofiles
|
public |
Implementation of gene expression anti-profiles
|
2024-12-14 |
bioconductor-swathxtend
|
public |
SWATH extended library generation and statistical data analysis
|
2024-12-14 |
bioconductor-metacca
|
public |
Summary Statistics-Based Multivariate Meta-Analysis of Genome-Wide Association Studies Using Canonical Correlation Analysis
|
2024-12-14 |
bioconductor-rnaseqcomp
|
public |
Benchmarks for RNA-seq Quantification Pipelines
|
2024-12-14 |
bioconductor-iaseq
|
public |
iASeq: integrating multiple sequencing datasets for detecting allele-specific events
|
2024-12-14 |
bioconductor-pepxmltab
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public |
Parsing pepXML files and filter based on peptide FDR.
|
2024-12-14 |
bioconductor-rlmm
|
public |
A Genotype Calling Algorithm for Affymetrix SNP Arrays
|
2024-12-14 |
bioconductor-mergeomics
|
public |
Integrative network analysis of omics data
|
2024-12-14 |
bioconductor-dyndoc
|
public |
Dynamic document tools
|
2024-12-14 |