bioconda / packages

Package Name Access Summary Updated
bioconductor-dupradar public Duplication rate quality control for RNA-Seq datasets. 2019-04-17
r-seurat public A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, and Butler A and Satija R (2017) <doi:10.1101/164889> for more details. 2019-04-16
r-phytools public A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research. 2019-04-09
r-hemdag public An implementation of Hierarchical Ensemble Methods for Directed Acyclic Graphs (DAGs). The 'HEMDAG' package can be used to enhance the predictions of virtually any flat learning methods, by taking into account the hierarchical nature of the classes of a bio-ontology. 'HEMDAG' is specifically designed for exploiting the hierarchical relationships of DAG-structured taxonomies, such as the Human Phenotype Ontology (HPO) or the Gene Ontology (GO), but it can be also safely applied to tree-structured taxonomies (as FunCat), since trees are DAGs. 'HEMDAG' scale nicely both in terms of the complexity of the taxonomy and in the cardinality of the examples. (Marco Notaro, Max Schubach, Peter N. Robinson and Giorgio Valentini (2017) <doi:10.1186/s12859-017-1854-y>). 2019-04-04
bioconductor-rhdf5 public This package provides an interface between HDF5 and R. HDF5's main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM. 2019-03-24
bioconductor-tofsims public This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing package EBImage offers image segmentation functionality. 2019-03-19
bioconductor-tweedeseq public Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions. 2019-03-17
bioconductor-cnordt public This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge. 2019-03-17
bioconductor-scater public A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization. 2019-03-17
bioconductor-edda public EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. This work was published on 3 December 2014 at Genome Biology under the title "The importance of study design for detecting differentially abundant features in high-throughput experiments" (http://genomebiology.com/2014/15/12/527). 2019-03-17
bioconductor-slalom public slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors. 2019-03-17
bioconductor-sspa public General Sample size and power analysis for microarray and next-generation sequencing data. 2019-03-17
bioconductor-mimosa public Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays. 2019-03-17
bioconductor-dexus public DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power. 2019-03-17
r-rtfbs public Identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by G+C content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R. 2019-03-13
bioconductor-cohcapanno public Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms 2019-03-13
bioconductor-rama public Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance. 2019-03-13
r-rgbif public A programmatic interface to the Web Service methods provided by the Global Biodiversity Information Facility ('GBIF'; <https://www.gbif.org/developer/summary>). 'GBIF' is a database of species occurrence records from sources all over the globe. 'rgbif' includes functions for searching for taxonomic names, retrieving information on data providers, getting species occurrence records, getting counts of occurrence records, and using the 'GBIF' tile map service to make 'rasters' summarizing huge amounts of data. 2019-03-13
bioconductor-abseqr public AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output. 2019-03-13
bioconductor-pd.u133.x3p public Platform Design Info for The Manufacturer's Name U133_X3P 2019-03-13
bioconductor-pd.moe430a public Platform Design Info for The Manufacturer's Name MOE430A 2019-03-13
bioconductor-pd.medicago public Platform Design Info for The Manufacturer's Name Medicago 2019-03-13
bioconductor-pd.atdschip.tiling public Platform Design Info for Affymetrix Atdschip_tiling 2019-03-13
bioconductor-pd.canine public Platform Design Info for The Manufacturer's Name Canine 2019-03-13
bioconductor-pd.s.aureus public Platform Design Info for The Manufacturer's Name S_aureus 2019-03-13
bioconductor-pd.mg.u74bv2 public Platform Design Info for The Manufacturer's Name MG_U74Bv2 2019-03-13
bioconductor-pd.hugene.1.1.st.v1 public Platform Design Info for Affymetrix HuGene-1_1-st-v1 2019-03-13
bioconductor-pd.zebgene.1.1.st public Platform Design Info for Affymetrix ZebGene-1_1-st 2019-03-13
bioconductor-pd.moex.1.0.st.v1 public Platform Design Info for Affymetrix MoEx-1_0-st-v1 2019-03-13
bioconductor-pd.zebrafish public Platform Design Info for The Manufacturer's Name Zebrafish 2019-03-13
bioconductor-pd.e.coli.2 public Platform Design Info for The Manufacturer's Name E_coli_2 2019-03-12
bioconductor-pd.ecoli.asv2 public Platform Design Info for The Manufacturer's Name Ecoli_ASv2 2019-03-12
bioconductor-pd.rjpgene.1.0.st public Platform Design Info for Affymetrix RJpGene-1_0-st 2019-03-12
bioconductor-pd.nugo.hs1a520180 public Platform Design Info for The Manufacturer's Name NuGO_Hs1a520180 2019-03-12
bioconductor-pd.mogene.1.1.st.v1 public Platform Design Info for Affymetrix MoGene-1_1-st-v1 2019-03-12
bioconductor-pd.rcngene.1.1.st public Platform Design Info for Affymetrix RCnGene-1_1-st 2019-03-12
bioconductor-pd.ragene.1.1.st.v1 public Platform Design Info for Affymetrix RaGene-1_1-st-v1 2019-03-12
bioconductor-pd.drogene.1.0.st public Platform Design Info for Affymetrix DroGene-1_0-st 2019-03-12
bioconductor-pd.ragene.2.0.st public Platform Design Info for Affymetrix RaGene-2_0-st 2019-03-12
bioconductor-pd.bovgene.1.0.st public Platform Design Info for Affymetrix BovGene-1_0-st 2019-03-12
bioconductor-pd.wheat public Platform Design Info for The Manufacturer's Name wheat 2019-03-12
bioconductor-qpcrnorm public The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available. 2019-03-12
bioconductor-maqcsubsetafx public MAQC data subset for the Affymetrix platform 2019-03-12
bioconductor-agimicrorna public Processing and Analysis of Agilent microRNA data 2019-03-12
bioconductor-bronchialil13 public derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549 2019-03-12
bioconductor-turbonorm public A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. 2019-03-12
bioconductor-lmgene public LMGene package for analysis of microarray data using a linear model and glog data transformation 2019-03-12
bioconductor-rpa public Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays. 2019-03-12
bioconductor-ipo public The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models. 2019-03-12
bioconductor-mait public The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions. 2019-03-12
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