Package ‘ sSeq ’ January 15 , 2017
نویسنده
چکیده
Maintainer Danni Yu Depends R (>= 3.0), caTools, RColorBrewer Description The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.
منابع مشابه
sSeq: A Simple and Shrinkage Approach of Differential Expression Analysis for RNA-Seq experiments
In this section, we will use the Hammer et. al. data [1] to illustrate how to use the functions in the sSeq package. The two conditions are control Sprague Dawley after 2 months (Condition A) and L5 SNL Sprague Dawley after 2 months (Condition B). There are two samples within each condition. This data is included in the sSeq package as an example, and can be imported as follows. “countsTable” i...
متن کاملPsychological and interactional characteristics of patients with somatoform disorders: Validation of the Somatic Symptoms Experiences Questionnaire (SSEQ) in a clinical psychosomatic population.
OBJECTIVE The new DSM-5 Somatic Symptom Disorder (SSD) emphasizes the importance of psychological processes related to somatic symptoms in patients with somatoform disorders. To address this, the Somatic Symptoms Experiences Questionnaire (SSEQ), the first self-report scale that assesses a broad range of psychological and interactional characteristics relevant to patients with a somatoform diso...
متن کاملPackage ‘ sSeq ’
Maintainer Danni Yu Depends R (>= 3.0), caTools, RColorBrewer Description The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The meth...
متن کاملPackage ‘ scran ’ January 15 , 2017
January 15, 2017 Version 1.2.1 Date 2017-01-11 Title Methods for Single-Cell RNA-Seq Data Analysis Maintainer Aaron Lun Depends R (>= 3.3.0), BiocParallel, scater Imports dynamicTreeCut, zoo, edgeR, stats, BiocGenerics, methods, Biobase, utils, Matrix, shiny, graphics, grDevices, statmod Suggests limSolve, limma, testthat, knitr, BiocStyle, org.Mm.eg.db, DESeq2, monocle, S4Ve...
متن کاملPackage 'paircompviz' Title Multiple Comparison Test Visualization
January 15, 2017 Type Package Title Multiple comparison test visualization Version 1.12.0 Date 2013-06-01 Author Michal Burda Maintainer Michal Burda Description This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized a...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
دوره شماره
صفحات -
تاریخ انتشار 2017