Ecosyste.ms: Papers
An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.
Projects: bioconductor: BitSeq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/BitSeq
Papers Mentioning BitSeq 28
10.1186/s13059-016-0881-8
A survey of best practices for RNA-seq data analysisCited 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 quantificationCited 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 genomicsCited by: 105
Author(s): Małgorzata Nowicka, Mark D. Robinson
Software Mentions: 14
Published: almost 8 years ago
10.1186/s12859-016-1457-z
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-SeqCited 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 dataCited 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 inferencesCited by: 795
Author(s): Charlotte Soneson, Michael I. Love, Mark D. Robinson
Software Mentions: 9
Published: over 8 years ago
10.1186/1471-2105-14-219
TCC: an R package for comparing tag count data with robust normalization strategiesCited 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 NormalizationCited 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 analysisCited 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 dataCited by: 30
Author(s): Yingtao Bi, Ramana V. Davuluri
Software Mentions: 7
Published: about 11 years ago
10.1186/s13040-016-0099-z
SePIA: RNA and small RNA sequence processing, integration, and analysisCited 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 callsCited by: 26
Author(s): Paweł P. Łabaj, David P. Kreil
Software Mentions: 7
Published: almost 8 years ago
10.1186/s12859-018-2370-4
GPrank: an R package for detecting dynamic elements from genome-wide time seriesCited 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 entericaCited 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: about 3 years ago
10.1186/s12864-016-2745-8
An optimized protocol for generation and analysis of Ion Proton sequencing reads for RNA-SeqCited 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 EnvironmentCited 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 DataCited 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-regressionCited 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 expressionCited 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 DataCited 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 RNAsCited by: 84
Author(s): Dmytro Ustianenko, Josef Pasulka, Zuzana Feketová, Lukas Bednarik, Dagmar Zigáčková, Andrea Fořtová, Mihaela Zavolan, Štěpánka Vaňáčová
Software Mentions: 2
Published: about 8 years ago
10.1186/1471-2164-15-S10-S5
TIGAR2: sensitive and accurate estimation of transcript isoform expression with longer RNA-Seq readsCited by: 40
Author(s): Naoki Nariai, Kazuyuki Kojima, Tsuneyo Mimori, Yukuto Sato, Yosuke Kawai, Yumi Yamaguchi-Kabata, Masao Nagasaki
Software Mentions: 2
Published: almost 10 years ago
10.1371/journal.pone.0188936
Campylobacter jejuni transcriptome changes during loss of culturability in waterCited 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: almost 7 years ago
10.1186/s13059-015-0838-3
A genome-wide survey of DNA methylation in hexaploid wheatCited by: 76
Author(s): Laura‐Jayne Gardiner, Mark Quinton-Tulloch, Lisa Olohan, Jonathan Price, Neil Hall, Anthony Hall
Software Mentions: 1
Published: almost 9 years ago
10.1099/mgen.0.000075
Bayesian identification of bacterial strains from sequencing dataCited 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: about 8 years ago
10.1093/bioinformatics/btv483
Fast and accurate approximate inference of transcript expression from RNA-seq dataCited by: 31
Author(s): James Hensman, Panagiotis Papastamoulis, Peter Glaus, Antti Honkela, Magnus Rattray
Software Mentions: 1
Published: about 9 years ago
10.1038/s41598-019-44499-3
Effect of de novo transcriptome assembly on transcript quantificationCited 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 DataCited by: 61
Author(s): Christine Anyansi, Timothy J. Straub, Abigail L. Manson, Ashlee M. Earl, Thomas Abeel
Software Mentions: 1
Published: about 4 years ago