bioconda / packages

Package Name Access Summary Updated
bioconductor-maanova public Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree. 2018-12-14
bioconductor-keggdzpathwaysgeo public This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package. 2018-12-14
bioconductor-keggandmetacoredzpathwaysgeo public This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods. 2018-12-14
bioconductor-iyer517 public representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html 2018-12-14
bioconductor-iterclust public A framework for performing clustering analysis iteratively. 2018-12-14
comet-ms public Comet is a command line tool that does MS/MS database search. 2018-12-14
bioconductor-hybridmtest public Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs. 2018-12-14
selene-sdk public Framework for developing sequence-level deep learning networks. 2018-12-14
shmlast public conditional reciprocal best hits with LAST 2018-12-13
krakenuniq public Metagenomics classifier with unique k-mer counting for more specific results 2018-12-13
deepvariant public DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data 2018-12-13
abeona public A simple transcriptome assembler based on kallisto and Cortex graphs. 2018-12-13
concoct public Clustering cONtigs with COverage and ComposiTion 2018-12-13
galaxy-parsec public Command-line utilities to assist in interacting with Galaxy servers (http://galaxyproject.org/). 2018-12-13
seqmap public SeqMap is a tool for mapping large amount of oligonucleotide to the genome. 2018-12-13
bioconductor-hopach public The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering). 2018-12-13
bioconductor-hgu133plus2cellscore public The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object. 2018-12-13
mentalist public The MLST pipeline developed by the PathOGiST research group. 2018-12-13
bioconductor-hem public This package fits heterogeneous error models for analysis of microarray data 2018-12-13
bioconductor-help public The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications. 2018-12-13
bioconductor-harbchip public data from a yeast ChIP-chip experiment 2018-12-13
bioconductor-hapfabia public A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats. 2018-12-13
bioconductor-gsealm public Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics. 2018-12-13
bioconductor-gse62944 public TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub. 2018-12-13
bioconductor-golubesets public representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format 2018-12-13
bioconductor-sradb public The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata. 2018-12-13
bioconductor-geometadb public The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 . 2018-12-13
bioconductor-dyebiasexamples public Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32 2018-12-13
bioconductor-geoquery public The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor. 2018-12-13
advntr public A tool for genotyping Variable Number Tandem Repeats (VNTR) from sequence data 2018-12-13
bioconductor-genetclassifier public Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier. 2018-12-13
bioconductor-geneselectmmd public Gene selection based on a mixture of marginal distributions 2018-12-13
searchgui public SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda and OMSSA. 2018-12-13
bioconductor-generecommender public This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions. 2018-12-13
bioconductor-geneclassifiers public This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input. 2018-12-13
bioconductor-gaschyhs public Data from PMID 11102521 2018-12-13
bioconductor-gaga public Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package). 2018-12-13
bioconductor-flowtrans public Profile maximum likelihood estimation of parameters for flow cytometry data transformations. 2018-12-13
peptide-shaker public PeptideShaker is a search engine independent platform for interpretation of proteomics identification results from multiple search engines, currently supporting X!Tandem, MS-GF+, MS Amanda, OMSSA, MyriMatch, Comet, Tide, Mascot, Andromeda and mzIdentML. By combining the results from multiple search engines, while re-calculating PTM localization scores and redoing the protein inference, PeptideShaker attempts to give you the best possible understanding of your proteomics data! 2018-12-13
fastqc public A quality control tool for high throughput sequence data. 2018-12-13
tmalign public TM-align sequence-order independent protein structure alignment 2018-12-13
bioconductor-nbsplice public The package proposes a differential splicing evaluation method based on isoform quantification. It applies generalized linear models with negative binomial distribution to infer changes in isoform relative expression. 2018-12-13
bioconductor-emdomics public The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover's Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests. 2018-12-13
bioconductor-gatefinder public Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type. 2018-12-13
bioconductor-flowbin public Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers. 2018-12-13
bioconductor-flowfp public Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry. 2018-12-13
bioconductor-flowclust public Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. 2018-12-13
bioconductor-flowviz public Provides visualization tools for flow cytometry data. 2018-12-13
bioconductor-flowutils public Provides utilities for flow cytometry data. 2018-12-13
bioconductor-flowmatch public Matching cell populations and building meta-clusters and templates from a collection of FC samples. 2018-12-13
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