bioconductor: BitSeq | Projects | Ecosyste.ms: Papers

10.1186/s13059-016-0881-8

A survey of best practices for RNA-seq data analysis
Cited by: 1,691
Author(s): Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, A Mortazavi
Software Mentions: 21
Published: almost 9 years ago

10.12688/f1000research.15398.3

Swimming downstream: statistical analysis of differential transcript usage following Salmon quantification
Cited by: 53
Author(s): Michael I. Love, Charlotte Soneson, Rob Patro
Software Mentions: 16
Published: about 6 years ago

10.12688/f1000research.8900.2

DRIMSeq: a Dirichlet-multinomial framework for multivariate count outcomes in genomics
Cited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: about 8 years ago

10.1186/s12859-016-1457-z

Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq
Cited by: 55
Author(s): Claire Williams, Alyssa Baccarella, Jay Z. Parrish, Charles C. Kim
Software Mentions: 13
Published: almost 8 years ago

10.1186/s13059-015-0702-5

Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data
Cited by: 128
Author(s): Alexander Kanitz, Foivos Gypas, Andreas Gruber, Andreas Gruber, Georges Martín, Mihaela Zavolan
Software Mentions: 9
Published: over 9 years ago

10.12688/f1000research.7563.2

Differential analyses for RNA-seq: transcript-level estimates improve gene-level inferences
Cited by: 795
Author(s): Charlotte Soneson, Michael I. Love, Mark D. Robinson
Software Mentions: 9
Published: almost 9 years ago

10.1186/1471-2105-14-219

TCC: an R package for comparing tag count data with robust normalization strategies
Cited by: 394
Author(s): Jianqiang Sun, Tomoaki Nishiyama, Kentaro Shimizu, Koji Kadota
Software Mentions: 8
Published: over 11 years ago

10.1155/2015/789516

Differential Expression Analysis in RNA-Seq by a Naive Bayes Classifier with Local Normalization
Cited by: 6
Author(s): Yongchao Dou, Xiaoli Guo, Lingling Yuan, David R. Holding, Chi Zhang
Software Mentions: 8
Published: almost 10 years ago

10.7717/peerj.1360

Getting the most out of RNA-seq data analysis
Cited by: 22
Author(s): Tsung Fei Khang, Ching Yee Lau
Software Mentions: 8
Published: about 9 years ago

10.1186/1471-2105-14-262

NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data
Cited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: over 11 years ago

10.1186/s13040-016-0099-z

SePIA: RNA and small RNA sequence processing, integration, and analysis
Cited by: 22
Author(s): Katherine Icay, Ping Chen, Alejandra Cervera, Ville Rantanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 7
Published: over 8 years ago

10.1186/s13062-016-0169-7

Sensitivity, specificity, and reproducibility of RNA-Seq differential expression calls
Cited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: about 8 years ago

10.1186/s12859-018-2370-4

GPrank: an R package for detecting dynamic elements from genome-wide time series
Cited by: 7
Author(s): Hande Topa, Antti Honkela
Software Mentions: 7
Published: about 6 years ago

10.1371/journal.ppat.1009280

Intracellular niche-specific profiling reveals transcriptional adaptations required for the cytosolic lifestyle of Salmonella enterica
Cited by: 29
Author(s): TuShun R. Powers, Amanda L. Haeberle, Alexander V. Predeus, Disa L. Hammarlöf, Jennifer A. Cundiff, Zeus Saldaña‐Ahuactzi, Karsten Hokamp, Jay C. D. Hinton, Leigh A. Knodler
Software Mentions: 6
Published: over 3 years ago

10.1186/s12864-016-2745-8

An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-Seq
Cited by: 17
Author(s): Yongxian Yuan, Huaiqian Xu, Rufina Leung
Software Mentions: 5
Published: over 8 years ago

10.1074/mcp.RA120.002175

Transcriptome and Secretome Analysis of Intra-Mammalian Life-Stages of Calicophoron daubneyi Reveals Adaptation to a Unique Host Environment
Cited by: 3
Author(s): Kathryn M. Huson, Erwan Atcheson, Nicola A.M. Oliver, Philip M. Best, J.P. Barley, R.E.B. Hanna, Tom N. McNeilly, Yongxiang Fang, Sam Haldenby, Steve Paterson, Mark W. Robinson
Software Mentions: 5
Published: almost 4 years ago

10.1111/rssc.12213

A Bayesian Model Selection Approach for Identifying Differentially Expressed Transcripts from RNA Sequencing Data
Cited by: 5
Author(s): Panagiotis Papastamoulis, Magnus Rattray
Software Mentions: 4
Published: almost 8 years ago

10.1186/s12859-015-0623-z

MetaDiff: differential isoform expression analysis using random-effects meta-regression
Cited by: 7
Author(s): Jia Cheng, Weihua Guan, Amy Yang, Rui Xiao, W.H. Wilson Tang, Christine S. Moravec, Kenneth B. Margulies, Thomas P. Cappola, Mingyao Li, Chun G Li
Software Mentions: 4
Published: over 9 years ago

10.1371/journal.pcbi.1006453

Telescope: Characterization of the retrotranscriptome by accurate estimation of transposable element expression
Cited by: 81
Author(s): Matthew L. Bendall, Miguel de Mulder, Luis P. Íñiguez, Aarón Lecanda, Marcos Pérez‐Losada, Mario Ostrowski, R. Brad Jones, Lubbertus C. F. Mulder, Gustavo Reyes‐Terán, Keith A. Crandall, Christopher E. Ormsby, Douglas F. Nixon
Software Mentions: 4
Published: about 5 years ago

10.1371/journal.pone.0140032

Modeling Exon-Specific Bias Distribution Improves the Analysis of RNA-Seq Data
Cited by: 1
Author(s): Xuejun Liu, Li Zhang, Songcan Chen
Software Mentions: 3
Published: about 9 years ago

10.15252/embj.201694857

TUT‐DIS3L2 is a mammalian surveillance pathway for aberrant structured non‐coding RNAs
Cited by: 84
Author(s): Dmytro Ustianenko, Josef Pasulka, Zuzana Feketová, Lukas Bednarik, Dagmar Zigáčková, Andrea Fořtová, Mihaela Zavolan, Štěpánka Vaňáčová
Software Mentions: 2
Published: over 8 years ago

10.1186/1471-2164-15-S10-S5

TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq reads
Cited by: 40
Author(s): Naoki Nariai, Kazuyuki Kojima, Tsuneyo Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
Software Mentions: 2
Published: about 10 years ago

10.1371/journal.pone.0188936

Campylobacter jejuni transcriptome changes during loss of culturability in water
Cited by: 13
Author(s): Christina Bronowski, Kasem Mustafa, Ian Goodhead, Chloë E. James, Charlotte Nelson, Anita Lucaci, Paul Wigley, Tom J. Humphrey, Nicola Williams, Craig Winstanley
Software Mentions: 1
Published: about 7 years ago

10.1186/s13059-015-0838-3

A genome-wide survey of DNA methylation in hexaploid wheat
Cited by: 76
Author(s): Laura‐Jayne Gardiner, Mark Quinton-Tulloch, Lisa Olohan, Jonathan Price, Neil Hall, Anthony Hall
Software Mentions: 1
Published: about 9 years ago

10.1099/mgen.0.000075

Bayesian identification of bacterial strains from sequencing data
Cited by: 17
Author(s): Aravind Sankar, Brandon Malone, Sion C. Bayliss, Ben Pascoe, Guillaume Méric, Matthew D. Hitchings, Samuel K. Sheppard, Edward J. Feil, Jukka Corander, Antti Honkela
Software Mentions: 1
Published: over 8 years ago

10.1093/bioinformatics/btv483

Fast and accurate approximate inference of transcript expression from RNA-seq data
Cited by: 31
Author(s): James Hensman, Panagiotis Papastamoulis, Peter Glaus, Antti Honkela, Magnus Rattray
Software Mentions: 1
Published: over 9 years ago

10.1038/s41598-019-44499-3

Effect of de novo transcriptome assembly on transcript quantification
Cited by: 34
Author(s): Ping-Han Hsieh, Yen-Jen Oyang, Chien‐Yu Chen
Software Mentions: 1
Published: over 5 years ago

10.3389/fmicb.2020.01925

Computational Methods for Strain-Level Microbial Detection in Colony and Metagenome Sequencing Data
Cited by: 61
Author(s): Christine Anyansi, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel
Software Mentions: 1
Published: over 4 years ago

Ecosyste.ms: Papers

Projects: bioconductor: BitSeq

Papers Mentioning BitSeq 28