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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-methylmix
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public |
MethylMix: Identifying methylation driven cancer genes
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2024-12-14 |
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bioconductor-limmagui
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public |
GUI for limma Package With Two Color Microarrays
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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-stattarget
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public |
Statistical Analysis of Molecular Profiles
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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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snostrip
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public |
Automatic snoRNA annotation pipeline
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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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pybedgraph
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public |
A package for fast operations on 1-dimensional genomic signal tracks
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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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bioconductor-gwas.bayes
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public |
Bayesian analysis of Gaussian GWAS data
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2024-12-14 |
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bioconductor-levi
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public |
Landscape Expression Visualization Interface
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2024-12-14 |
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bioconductor-hubpub
|
public |
Utilities to create and use Bioconductor Hubs
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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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bioconductor-wrench
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public |
Wrench normalization for sparse count data
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2024-12-14 |
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mantis_pfa
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public |
Consensus-driven protein function annotation tool
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2024-12-14 |
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bioconductor-tkwidgets
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public |
R based tk widgets
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2024-12-14 |
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bioconductor-isocorrectorgui
|
public |
Graphical User Interface for IsoCorrectoR
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2024-12-14 |
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r-cobrar
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public |
COnstraint-based Reconstruction and Analysis (COBRA) of metabolic networks in R
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2024-12-14 |
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bioconductor-samspectral
|
public |
Identifies cell population in flow cytometry data
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2024-12-14 |
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hla-la
|
public |
HLA typing from short and long reads
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2024-12-14 |
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cpat
|
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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fegenie
|
public |
HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes.
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2024-12-14 |
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d4tools
|
public |
The D4 command line utility program
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2024-12-14 |
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metaphyler
|
public |
No Summary
|
2024-12-14 |
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trumicount
|
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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d4binding
|
public |
The C/C++ binding for the D4 file format.
|
2024-12-14 |
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libmaus2
|
public |
Collection of data structures and algorithms for NGS data.
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2024-12-14 |
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mykatlas
|
public |
Assists in discoveries of antibiotic-resistance with mykrobe
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2024-12-14 |
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das_tool
|
public |
Recovery of genomes from metagenomes via a dereplication,
aggregation and scoring strategy.
|
2024-12-14 |
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r-eztune
|
public |
Contains two functions that are intended to make tuning supervised learning methods easy. The eztune function uses a genetic algorithm or Hooke-Jeeves optimizer to find the best set of tuning parameters. The user can choose the optimizer, the learning method, and if optimization will be based on accuracy obtained through validation error, cross validation, or resubstitution. The function eztune.cv will compute a cross validated error rate. The purpose of eztune_cv is to provide a cross validated accuracy or MSE when resubstitution or validation data are used for optimization because error measures from both approaches can be misleading.
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2024-12-14 |
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bioconductor-intramirexplorer
|
public |
Predicting Targets for Drosophila Intragenic miRNAs
|
2024-12-14 |
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pybedlite
|
public |
Lightweight python classes for interfacing with bed intervals
|
2024-12-14 |
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bioconductor-rbwa
|
public |
R wrapper for BWA-backtrack and BWA-MEM aligners
|
2024-12-14 |
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bioconductor-sparsematrixstats
|
public |
Summary Statistics for Rows and Columns of Sparse Matrices
|
2024-12-14 |
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cassiopeia
|
public |
The Cython compiler for writing C extensions in the Python language.
|
2024-12-14 |
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bioconductor-biocworkflowtools
|
public |
Tools to aid the development of Bioconductor Workflow packages
|
2024-12-14 |
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bioconductor-illuminaio
|
public |
Parsing Illumina Microarray Output Files
|
2024-12-14 |
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short-read-connector
|
public |
Short read connector enables the comparisons of two read sets
|
2024-12-14 |
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bioconductor-hyper
|
public |
An R Package For Geneset Enrichment Workflows
|
2024-12-14 |
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bioconductor-process
|
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
|
public |
fast, minimal, UTF-8-only serialization of data to JSON
|
2024-12-14 |
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ginpiper
|
public |
Package for smooth curve estimation, R_e computation and plotting.
|
2024-12-14 |
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perl-extutils-cppguess
|
public |
guess C++ compiler and flags
|
2024-12-14 |
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bioconductor-fmrs
|
public |
Variable Selection in Finite Mixture of AFT Regression and FMR Models
|
2024-12-14 |
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bioconductor-dcats
|
public |
Differential Composition Analysis Transformed by a Similarity matrix
|
2024-12-14 |
