Пакунок: r-bioc-fishpond (2.10.0+ds-1)

[ Source: r-bioc-fishpond  ]

Differential transcript and gene expression with inferential replicates

Fishpond contains methods for differential transcript and gene expression analysis of RNA-seq data using inferential replicates for uncertainty of abundance quantification, as generated by Gibbs sampling or bootstrap sampling. Also the package contains utilities for working with Salmon and Alevin quantification files.

Інші пакунки пов'язані з r-bioc-fishpond

• dep: r-api-4.0

  virtual package provided by r-base-core

• dep: r-api-bioc-3.19

  virtual package provided by r-bioc-biocgenerics

• dep: r-bioc-genomicranges (>= 1.56.1)

  BioConductor representation and manipulation of genomic intervals

• dep: r-bioc-iranges (>= 2.38.1)

  GNU R low-level containers for storing sets of integer ranges

• dep: r-bioc-qvalue (>= 2.36.0)

  GNU R package for Q-value estimation for FDR control

• dep: r-bioc-s4vectors (>= 0.42.1)

  BioConductor S4 implementation of vectors and lists

• dep: r-bioc-singlecellexperiment (>= 1.26.0)

  S4 Classes for Single Cell Data

• dep: r-bioc-summarizedexperiment (>= 1.34.0)

  BioConductor assay container

• dep: r-cran-abind

  GNU R abind multi-dimensional array combination function

• dep: r-cran-gtools

  GNU R package with R programming tools by Greg Warnes et al

• dep: r-cran-jsonlite

  Robust, High Performance JSON Parser and Generator for R

• dep: r-cran-matrix

  GNU R package of classes for dense and sparse matrices

• dep: r-cran-matrixstats

  GNU R methods that apply to rows and columns of a matrix

• dep: r-cran-svmisc

  SciViews - Miscellaneous Functions

• sug: r-bioc-annotationdbi (>= 1.66.0)

  GNU R Annotation Database Interface for BioConductor

• sug: r-bioc-deseq2 (>= 1.44.0)

  R package for RNA-Seq Differential Expression Analysis

• sug: r-bioc-ensembldb (>= 2.28.0)

  GNU R utilities to create and use an Ensembl based annotation database

• sug: r-bioc-genomeinfodb (>= 1.40.1)

  BioConductor utilities for manipulating chromosome identifiers

• sug: r-bioc-genomicfeatures (>= 1.56.0)

  GNU R tools for making and manipulating transcript centric annotations

• sug: r-bioc-gviz (>= 1.48.0)

  Plotting data and annotation information along genomic coordinates

• sug: r-bioc-limma (>= 3.60.4)

  linear models for microarray data

• sug: r-bioc-org.hs.eg.db (>= 3.19.1)

  genome-wide annotation for Human

• sug: r-bioc-tximeta (>= 1.22.1)

  Transcript Quantification Import with Automatic Metadata

• sug: r-bioc-tximportdata (>= 1.32.0)

  GNU R various transcript abundance quantifiers

• sug: r-cran-data.table

  GNU R extension of Data.frame

• sug: r-cran-knitr

  GNU R package for dynamic report generation using Literate Programming

• sug: r-cran-pheatmap

  GNU R package to create pretty heatmaps

• sug: r-cran-rmarkdown

  convert R markdown documents into a variety of formats

• sug: r-cran-samr

  GNU R significance analysis of microarrays

• sug: r-cran-testthat

  GNU R testsuite

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