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andi
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public |
Efficient Estimation of Evolutionary Distances
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2024-12-14 |
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bioconductor-absseq
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public |
ABSSeq: a new RNA-Seq analysis method based on modelling absolute expression differences
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2024-12-14 |
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bioconductor-massspecwavelet
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public |
Peak Detection for Mass Spectrometry data using wavelet-based algorithms
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2024-12-14 |
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r-pscbs
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public |
Segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported.
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2024-12-14 |
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r-metama
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public |
Combines either p-values or modified effect sizes from different studies to find differentially expressed genes
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2024-12-14 |
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bioconductor-minet
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public |
Mutual Information NETworks
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2024-12-14 |
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bioconductor-deqms
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public |
a tool to perform statistical analysis of differential protein expression for quantitative proteomics data.
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2024-12-14 |
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perl-aceperl
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public |
Object-Oriented Access to ACEDB Databases
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2024-12-14 |
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bioconductor-marray
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public |
Exploratory analysis for two-color spotted microarray data
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2024-12-14 |
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bioconductor-ichip
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public |
Bayesian Modeling of ChIP-chip Data Through Hidden Ising Models
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2024-12-14 |
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bioconductor-rprotobuflib
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public |
C++ headers and static libraries of Protocol buffers
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2024-12-14 |
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bioconductor-multiclust
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public |
multiClust: An R-package for Identifying Biologically Relevant Clusters in Cancer Transcriptome Profiles
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2024-12-14 |
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bioconductor-icobra
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public |
Comparison and Visualization of Ranking and Assignment Methods
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2024-12-14 |
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r-speaq
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public |
Makes Nuclear Magnetic Resonance spectroscopy (NMR spectroscopy) data analysis as easy as possible by only requiring a small set of functions to perform an entire analysis. 'speaq' offers the possibility of raw spectra alignment and quantitation but also an analysis based on features whereby the spectra are converted to peaks which are then grouped and turned into features. These features can be processed with any number of statistical tools either included in 'speaq' or available elsewhere on CRAN. More detail can be found in Vu et al. (2011) <doi:10.1186/1471-2105-12-405> and Beirnaert et al. (2018) <doi:10.1371/journal.pcbi.1006018>.
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2024-12-14 |
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bioconductor-edger
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public |
Empirical Analysis of Digital Gene Expression Data in R
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2024-12-14 |
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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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2024-12-14 |
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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 |
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cpat
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public |
Coding Potential Assessment Tool
|
2024-12-14 |
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bioconductor-beaddatapackr
|
public |
Compression of Illumina BeadArray data
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2024-12-14 |
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metaphyler
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public |
No Summary
|
2024-12-14 |
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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 |
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perl-class-methodmaker
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public |
Create generic methods for OO Perl
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2024-12-14 |
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mykatlas
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public |
Assists in discoveries of antibiotic-resistance with mykrobe
|
2024-12-14 |
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das_tool
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public |
Recovery of genomes from metagenomes via a dereplication,
aggregation and scoring strategy.
|
2024-12-14 |
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bioconductor-biocworkflowtools
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public |
Tools to aid the development of Bioconductor Workflow packages
|
2024-12-14 |
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bioconductor-illuminaio
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public |
Parsing Illumina Microarray Output Files
|
2024-12-14 |
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bioconductor-process
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public |
Ciphergen SELDI-TOF Processing
|
2024-12-14 |
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bioconductor-harman
|
public |
The removal of batch effects from datasets using a PCA and constrained optimisation based technique
|
2024-12-14 |
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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 |
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perl-extutils-cppguess
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public |
guess C++ compiler and flags
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2024-12-14 |
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infernal
|
public |
Infernal is for searching DNA sequence databases for RNA structure and sequence similarities.
|
2024-12-14 |
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r-facets
|
public |
Cellular Fraction and Copy Numbers from Tumor Sequencing
|
2024-12-14 |
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fermi2
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public |
Fermi2 focuses on the exploration of FMD-index as a graph.
|
2024-12-14 |
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ucsc-websync
|
public |
download from https server, using files.txt on their end to get the list of files
|
2024-12-14 |
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perl-devel-size
|
public |
Perl extension for finding the memory usage of Perl variables
|
2024-12-14 |
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bioconductor-unifiedwmwqpcr
|
public |
Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data
|
2024-12-14 |
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ucsc-chopfalines
|
public |
Read in FA file with long lines and rewrite it with shorter lines
|
2024-12-14 |
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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 |
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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 |
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bioconductor-preprocesscore
|
public |
A collection of pre-processing functions
|
2024-12-14 |
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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 |
