Package: ROSeq 1.19.0

Krishan Gupta

ROSeq: Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq data

ROSeq - A rank based approach to modeling gene expression with filtered and normalized read count matrix. ROSeq takes filtered and normalized read matrix and cell-annotation/condition as input and determines the differentially expressed genes between the contrasting groups of single cells. One of the input parameters is the number of cores to be used.

Authors:Krishan Gupta [aut, cre], Manan Lalit [aut], Aditya Biswas [aut], Abhik Ghosh [aut], Debarka Sengupta [aut]

ROSeq_1.19.0.tar.gz
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ROSeq.pdf |ROSeq.html✨
ROSeq/json (API)
NEWS

# Install 'ROSeq' in R:
install.packages('ROSeq', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/krishan57gupta/roseq/issues

Datasets:

On BioConductor:ROSeq-1.19.0(bioc 3.21)ROSeq-1.18.0(bioc 3.20)

geneexpressiondifferentialexpressionsinglecellcount-datagene-expressiongene-expression-profilesnormalizationpopulationsranktmmtungtung-datasettutorialvignette

4.34 score 2 stars 11 scripts 188 downloads 2 exports 6 dependencies

Last updated 2 months agofrom:f033b59032. Checks:OK: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 04 2024
R-4.5-winWARNINGDec 04 2024
R-4.5-linuxWARNINGDec 04 2024
R-4.4-winWARNINGDec 04 2024
R-4.4-macWARNINGDec 04 2024
R-4.3-winWARNINGDec 04 2024
R-4.3-macWARNINGDec 04 2024

Exports:ROSeqTMMnormalization

Dependencies:edgeRlatticelimmalocfitpbmcapplystatmod

ROSeq

Rendered fromROSeq.Rmdusingknitr::rmarkdownon Dec 04 2024.

Last update: 2021-02-16
Started: 2019-12-04

Readme and manuals

Help Manual

Help pageTopics
Computes differential expression for the gene in question, by comparing the optimal parameters for sub-populations one and twocomputeDEG
Finds the optimal values of parameters a and b that model the probability distribution of ranks, by Maximising the Log-LikelihoodfindParams
Finds the double derivative of Agetd
Evaluates statistics of the read counts corresponding to the genegetDataStatistics
Finds the first derivative of u1 with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).getdu1da
Finds the first derivative of u1 with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).getdu1db
Finds the first derivative of u2 with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).getdu2da
Finds the first derivative of u2 with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).getdu2db
Finds the first derivative of v with respect to a. This first derivative is evaluated at the optimal (a_hat, b_hat).getdvda
Finds the first derivative of v with respect to b. This first derivative is evaluated at the optimal (a_hat, b_hat).getdvdb
Computes the Fisher Information MatrixgetI
Computes u1getu1
Computes u2getu2
Computes vgetv
Computes differential analysis for a given geneinitiateAnalysis
Single cell samples for DE genes analysisL_Tung_single
Minimizes the Negative Log-Likelihood by iterating across values of parameters a and bminimizeNLL
Modeling expression ranks for noise-tolerant differential expression analysis of scRNA-Seq dataROSeq
TMM Normalization.TMMnormalization