Cargando…

lmerSeq: an R package for analyzing transformed RNA-Seq data with linear mixed effects models

BACKGROUND: Studies that utilize RNA Sequencing (RNA-Seq) in conjunction with designs that introduce dependence between observations (e.g. longitudinal sampling) require specialized analysis tools to accommodate this additional complexity. This R package contains a set of utilities to fit linear mix...

Descripción completa

Detalles Bibliográficos
Autores principales:	Vestal, Brian E., Wynn, Elizabeth, Moore, Camille M.
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	BioMed Central 2022
Materias:	Software
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9670578/ https://www.ncbi.nlm.nih.gov/pubmed/36384492 http://dx.doi.org/10.1186/s12859-022-05019-9

Ejemplares similares

intePareto: an R package for integrative analyses of RNA-Seq and ChIP-Seq data
por: Cao, Yingying, et al.
Publicado: (2020)

GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases
por: Zhu, Lihua Julie, et al.
Publicado: (2017)

pcaExplorer: an R/Bioconductor package for interacting with RNA-seq principal components
por: Marini, Federico, et al.
Publicado: (2019)

GeneTonic: an R/Bioconductor package for streamlining the interpretation of RNA-seq data
por: Marini, Federico, et al.
Publicado: (2021)

ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data
por: Ihnatova, Ivana, et al.
Publicado: (2015)

ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions
por: Muiño, Jose M, et al.
Publicado: (2011)

spliceR: an R package for classification of alternative splicing and prediction of coding potential from RNA-seq data
por: Vitting-Seerup, Kristoffer, et al.
Publicado: (2014)

seqCNA: an R package for DNA copy number analysis in cancer using high-throughput sequencing
por: Mosen-Ansorena, David, et al.
Publicado: (2014)

The ChIP-Seq tools and web server: a resource for analyzing ChIP-seq and other types of genomic data
por: Ambrosini, Giovanna, et al.
Publicado: (2016)

IsomiR_Window: a system for analyzing small-RNA-seq data in an integrative and user-friendly manner
por: Vasconcelos, Ana M., et al.
Publicado: (2021)

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration
por: Leśniewska, Anna, et al.
Publicado: (2011)

An R package for analyzing and modeling ranking data
por: Lee, Paul H, et al.
Publicado: (2013)

Segmentor3IsBack: an R package for the fast and exact segmentation of Seq-data
por: Cleynen, Alice, et al.
Publicado: (2014)

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq
por: Wen, Bo, et al.
Publicado: (2016)

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data
por: Sayols, Sergi, et al.
Publicado: (2016)

GSEPD: a Bioconductor package for RNA-seq gene set enrichment and projection display
por: Stamm, Karl, et al.
Publicado: (2019)

CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data
por: duVerle, David A., et al.
Publicado: (2016)

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data
por: Ou, Jianhong, et al.
Publicado: (2018)

plotnineSeqSuite: a Python package for visualizing sequence data using ggplot2 style
por: Cao, Tianze, et al.
Publicado: (2023)

Ringo – an R/Bioconductor package for analyzing ChIP-chip readouts
por: Toedling, Joern, et al.
Publicado: (2007)

ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data
por: Zhu, Lihua J, et al.
Publicado: (2010)

FINDER: an automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences
por: Banerjee, Sagnik, et al.
Publicado: (2021)

SeqX: a tool to detect, analyze and visualize residue co-locations in protein and nucleic acid structures
por: Biro, Jan C, et al.
Publicado: (2005)

EPIG-Seq: extracting patterns and identifying co-expressed genes from RNA-Seq data
por: Li, Jianying, et al.
Publicado: (2016)

pROC: an open-source package for R and S+ to analyze and compare ROC curves
por: Robin, Xavier, et al.
Publicado: (2011)

Cascade: an RNA-seq visualization tool for cancer genomics
por: Shifman, Aaron R., et al.
Publicado: (2016)

HISS: Snakemake-based workflows for performing SMRT-RenSeq assembly, AgRenSeq and dRenSeq for the discovery of novel plant disease resistance genes
por: Adams, Thomas M., et al.
Publicado: (2023)

MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps
por: Khomtchouk, Bohdan B., et al.
Publicado: (2016)

ChiLin: a comprehensive ChIP-seq and DNase-seq quality control and analysis pipeline
por: Qin, Qian, et al.
Publicado: (2016)

VIPER: Visualization Pipeline for RNA-seq, a Snakemake workflow for efficient and complete RNA-seq analysis
por: Cornwell, MacIntosh, et al.
Publicado: (2018)

RiboPlotR: a visualization tool for periodic Ribo-seq reads
por: Wu, Hsin-Yen Larry, et al.
Publicado: (2021)

CPMCGLM: an R package for p-value adjustment when looking for an optimal transformation of a single explanatory variable in generalized linear models
por: Liquet, Benoit, et al.
Publicado: (2019)

ddSeeker: a tool for processing Bio-Rad ddSEQ single cell RNA-seq data
por: Romagnoli, Dario, et al.
Publicado: (2018)

cosinoRmixedeffects: an R package for mixed-effects cosinor models
por: Hou, Ruixue, et al.
Publicado: (2021)

De novo assembly of bacterial transcriptomes from RNA-seq data
por: Tjaden, Brian
Publicado: (2015)

ALGAEFUN with MARACAS, microALGAE FUNctional enrichment tool for MicroAlgae RnA-seq and Chip-seq AnalysiS
por: Romero-Losada, Ana B., et al.
Publicado: (2022)

DROPA: DRIP-seq optimized peak annotator
por: Russo, Marco, et al.
Publicado: (2019)

RASflow: an RNA-Seq analysis workflow with Snakemake
por: Zhang, Xiaokang, et al.
Publicado: (2020)

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
por: Ather, Syed Hussain, et al.
Publicado: (2020)

RiboProfiling: a Bioconductor package for standard Ribo-seq pipeline processing
por: Popa, Alexandra, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_a2cb5t5vru4r38rouhfugn75a8