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r-imputelcmd
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public |
The package contains a collection of functions for left-censored missing data imputation. Left-censoring is a special case of missing not at random (MNAR) mechanism that generates non-responses in proteomics experiments. The package also contains functions to artificially generate peptide/protein expression data (log-transformed) as random draws from a multivariate Gaussian distribution as well as a function to generate missing data (both randomly and non-randomly). For comparison reasons, the package also contains several wrapper functions for the imputation of non-responses that are missing at random. * New functionality has been added: a hybrid method that allows the imputation of missing values in a more complex scenario where the missing data are both MAR and MNAR.
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2024-12-18 |
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bioconductor-nucleosim
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public |
Generate synthetic nucleosome maps
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2024-12-18 |
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prophyle
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public |
ProPhyle is an accurate, resource-frugal and deterministic phylogeny-based metagenomic classifier.
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2024-12-18 |
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bioconductor-scde
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public |
Single Cell Differential Expression
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2024-12-18 |
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bioconductor-ebcoexpress
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public |
EBcoexpress for Differential Co-Expression Analysis
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2024-12-18 |
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r-aroma.affymetrix
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public |
A cross-platform R framework that facilitates processing of any number of Affymetrix microarray samples regardless of computer system. The only parameter that limits the number of chips that can be processed is the amount of available disk space. The Aroma Framework has successfully been used in studies to process tens of thousands of arrays. This package has actively been used since 2006.
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2024-12-18 |
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bioconductor-healthyflowdata
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public |
Healthy dataset used by the flowMatch package
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2024-12-18 |
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bioconductor-genetclassifier
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public |
Classify diseases and build associated gene networks using gene expression profiles
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2024-12-18 |
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bioconductor-mogamun
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public |
MOGAMUN: A Multi-Objective Genetic Algorithm to Find Active Modules in Multiplex Biological Networks
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2024-12-18 |
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bioconductor-orderedlist
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public |
Similarities of Ordered Gene Lists
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2024-12-18 |
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bioconductor-bumpymatrix
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public |
Bumpy Matrix of Non-Scalar Objects
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2024-12-18 |
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bioconductor-pvac
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public |
PCA-based gene filtering for Affymetrix arrays
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2024-12-18 |
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pb-falcon
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public |
FALCON/Unzip tool-suite (originally by Jason Chin)
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2024-12-18 |
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bioconductor-siggenes
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public |
Multiple Testing using SAM and Efron's Empirical Bayes Approaches
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2024-12-18 |
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r-ontologyplot
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public |
Functions for visualising sets of ontological terms using the 'graphviz' layout system.
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2024-12-18 |
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bioconductor-qpcrnorm
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public |
Data-driven normalization strategies for high-throughput qPCR data.
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2024-12-18 |
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bioconductor-kegggraph
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public |
KEGGgraph: A graph approach to KEGG PATHWAY in R and Bioconductor
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2024-12-18 |
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bioconductor-geosubmission
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public |
Prepares microarray data for submission to GEO
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2024-12-18 |
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bioconductor-diggit
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public |
Inference of Genetic Variants Driving Cellular Phenotypes
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2024-12-18 |
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bioconductor-gaga
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public |
GaGa hierarchical model for high-throughput data analysis
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2024-12-18 |
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umis
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public |
Tools for processing UMI RNA-tag data
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2024-12-18 |
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bioconductor-bronchialil13
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public |
time course experiment involving il13
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2024-12-18 |
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bioconductor-affyrnadegradation
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public |
Analyze and correct probe positional bias in microarray data due to RNA degradation
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2024-12-18 |
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bioconductor-ocplus
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public |
Operating characteristics plus sample size and local fdr for microarray experiments
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2024-12-18 |
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bioconductor-densvis
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public |
Density-Preserving Data Visualization via Non-Linear Dimensionality Reduction
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2024-12-18 |
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epic2
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public |
Ultraperformant Chip-Seq broad domain finder based on SICER.
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2024-12-18 |
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bioconductor-sconify
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public |
A toolkit for performing KNN-based statistics for flow and mass cytometry data
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2024-12-18 |
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bioconductor-biomvcclass
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public |
Model-View-Controller (MVC) Classes That Use Biobase
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2024-12-18 |
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r-structssi
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public |
Performs multiple testing corrections that take specific structure of hypotheses into account.
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2024-12-18 |
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perl-list-moreutils-xs
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public |
Provide the stuff missing in List::Util in XS
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2024-12-18 |
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bioconductor-flowai
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public |
Automatic and interactive quality control for flow cytometry data
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2024-12-18 |
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bioconductor-targetdecoy
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public |
Diagnostic Plots to Evaluate the Target Decoy Approach
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2024-12-18 |
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bioconductor-deconrnaseq
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public |
Deconvolution of Heterogeneous Tissue Samples for mRNA-Seq data
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2024-12-18 |
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bioconductor-affycompdata
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public |
affycomp data
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2024-12-18 |
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bioconductor-cardinalio
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public |
Read and write mass spectrometry imaging files
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2024-12-18 |
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bioconductor-mzr
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public |
parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data)
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2024-12-18 |
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pysam
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public |
Pysam is a Python module for reading and manipulating SAM/BAM/VCF/BCF files. It's a lightweight wrapper of the htslib C-API, the same one that powers samtools, bcftools, and tabix.
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2024-12-18 |
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deltapd
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public |
DeltaPD is a tool used to determine outliers in a gene tree when compared against a reference tree.
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2024-12-18 |
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r-genomictools.filehandler
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public |
A collection of I/O tools for handling the most commonly used genomic datafiles, like fasta/-q, bed, gff, gtf, ped/map and vcf.
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2024-12-18 |
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mutyper
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public |
A Python package and command line utility for annotating the local ancestral sequence context of biallelic SNPs.
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2024-12-18 |
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metamdbg
|
public |
MetaMDBG: a lightweight assembler for long and accurate metagenomics reads.
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2024-12-18 |
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bioconductor-matter
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public |
Out-of-core statistical computing and signal processing
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2024-12-18 |
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bioconductor-mzid
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public |
An mzIdentML parser for R
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2024-12-18 |
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lastz
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public |
LASTZ is a program for aligning DNA sequences, a pairwise aligner.
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2024-12-18 |
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centrosome
|
public |
An open source image processing library. Dependency for CellProfiler
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2024-12-18 |
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samsum
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public |
A light-weight python package for summarizing sequence coverage from SAM and BAM files
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2024-12-18 |
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bioconductor-protgenerics
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public |
Generic infrastructure for Bioconductor mass spectrometry packages
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2024-12-18 |
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rnashapes
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public |
RNAshape abstraction maps structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features, but disregarding helix lengths. Shape abstraction integrates well with dynamic programming algorithms, and hence it can be applied during structure prediction rather than afterwards. This avoids exponential explosion and can still give us a non-heuristic and complete account of properties of the molecule's folding space.
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2024-12-18 |
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acms
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public |
Ambivalent Covariance Models (aCMs) are our prototypic suggestion to extend CMs with more than one consensus structure.
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2024-12-18 |
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pkiss
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public |
RNA secondary structure prediction including K-type and kissing hairpin- pseudoknots.
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2024-12-18 |
