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: DRIMSeq
https://packages.ecosyste.ms/registries/bioconductor.org/packages/DRIMSeq
Differential transcript usage and tuQTL analyses with Dirichlet-multinomial model in RNA-seq
1 version
Latest release: about 1 year ago
1 dependent package
34,118 downloads total
Papers Mentioning DRIMSeq 17
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/s12859-019-3029-5
CAGEfightR: analysis of 5′-end data using R/BioconductorCited by: 35
Author(s): Malte Thodberg, Axel Thieffry, Kristoffer Vitting-Seerup, Robin Andersson, Albin Sandelin
Software Mentions: 13
Published: about 5 years ago
10.12688/f1000research.17082.2
Correction of gene model annotations improves isoform abundance estimates: the example of ketohexokinase (Khk)Cited by: 4
Author(s): Christophe D. Chabbert, Tanja Eberhart, Ilaria Guccini, Wilhelm Krek, Werner J. Kovacs
Software Mentions: 12
Published: over 5 years ago
10.1186/s13059-020-1935-5
Opportunities and challenges in long-read sequencing data analysisCited by: 1,295
Author(s): Shanika L. Amarasinghe, Shian Su, Xueyi Dong, Luke Zappia, Matthew E. Ritchie, Quentin Gouil
Software Mentions: 9
Published: almost 5 years ago
10.7554/eLife.69431
Inflammation drives alternative first exon usage to regulate immune genes including a novel iron-regulated isoform of Aim2Cited by: 18
Author(s): Elektra Kantzari Robinson, Pratibha Jagannatha, Sergio Covarrubias, Matthew Cattle, Valeriya Smaliy, Rojin Safavi, Barbara Shapleigh, Robin Abu-Shumays, Miten Jain, Suzanne M. Cloonan, Mark Akeson, Angela N. Brooks
Software Mentions: 9
Published: over 3 years ago
10.1534/g3.119.400185
ARMOR: An <u>A</u>utomated <u>R</u>eproducible <u>MO</u>dular Workflow for Preprocessing and Differential Analysis of <u>R</u>NA-seq DataCited by: 35
Author(s): Stephany Orjuela, Ronald Huang, Katharina Hembach, Mark D. Robinson, Charlotte Soneson
Software Mentions: 8
Published: over 5 years ago
10.12688/f1000research.17916.1
Relative Abundance of Transcripts (RATs): Identifying differential isoform abundance from RNA-seqCited by: 19
Author(s): Kimon Froussios, Kira Mourão, Gordon G. Simpson, Geoffrey J. Barton, Nicholas J. Schurch
Software Mentions: 7
Published: over 5 years ago
10.1186/s13195-020-00709-z
TREM2 Alzheimer’s variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophagesCited by: 25
Author(s): Hazel Hall‐Roberts, Devika Agarwal, Juliane Obst, Thomas B. Smith, Jimena Monzón‐Sandoval, Elena Di Daniel, Caleb Webber, William James, Emma Mead, John B. Davis, Sally A. Cowley
Software Mentions: 7
Published: about 4 years ago
10.3390/plants9121700
Transcriptome Analysis of Alternative Splicing Events Induced by Arbuscular Mycorrhizal Fungi (Rhizophagus irregularis) in Pea (Pisum sativum L.) RootsCited by: 8
Author(s): Evgeny A. Zorin, Alexey М. Afonin, Olga A. Kulaeva, Emma S. Gribchenko, O. Y. Shtark, Vladimir A. Zhukov
Software Mentions: 7
Published: almost 4 years ago
10.1016/j.cell.2021.07.018
TDP-43 condensation properties specify its RNA-binding and regulatory repertoireCited by: 99
Author(s): Martina Hallegger, Anob M. Chakrabarti, Flora Lee, Bo Lim Lee, Aram Gustav Amalietti, Hana M. Odeh, Katie E. Copley, Jack D. Rubien, Bede Portz, Klara Kuret, Ina Huppertz, Frédérique Rau, Rickie Patani, Nicolas L. Fawzi, James Shorter, Nicholas M. Luscombe, Jernej Ule
Software Mentions: 6
Published: about 3 years ago
10.1186/s13059-020-01967-8
BANDITS: Bayesian differential splicing accounting for sample-to-sample variability and mapping uncertaintyCited by: 16
Author(s): Simone Tiberi, Mark D. Robinson
Software Mentions: 6
Published: over 4 years ago
10.12688/f1000research.18276.2
Using equivalence class counts for fast and accurate testing of differential transcript usageCited by: 9
Author(s): Marek Cmero, N. Davidson, Alicia Oshlack
Software Mentions: 5
Published: over 5 years ago
10.3389/fcell.2021.671806
Knockdown of Splicing Complex Protein PCBP2 Reduces Extravillous Trophoblast Differentiation Through Transcript SwitchingCited by: 6
Author(s): Danai Georgiadou, Souad Boussata, Remco Keijser, Dianta Janssen, Gijs B. Afink, Marie van Dijk
Software Mentions: 4
Published: over 3 years ago
10.1038/s41598-019-54782-y
Investigating the energy crisis in Alzheimer disease using transcriptome studyCited by: 21
Author(s): S. Akila Parvathy Dharshini, Y-h. Taguchi, M. Michael Gromiha
Software Mentions: 4
Published: almost 5 years ago
10.7554/eLife.50895
Partial loss of CFIm25 causes learning deficits and aberrant neuronal alternative polyadenylationCited by: 23
Author(s): Callison E Alcott, Hari Krishna Yalamanchili, Ping Ji, Meike E van der Heijden, Alexander B. Saltzman, Nathan D. Elrod, Lin Ai, Mei Leng, Bhoomi Bhatt, Shuang Hao, Qi Wang, Afaf Saliba, Jianrong Tang, Anna Malovannaya, Eric J. Wagner, Zhandong Liu, Huda Y. Zoghbi
Software Mentions: 4
Published: over 4 years ago
10.1371/journal.pgen.1009182
Differential transcript usage in the Parkinson’s disease brainCited by: 12
Author(s): Fiona Dick, Gonzalo S. Nido, Guido Alves, Ole‐Bjørn Tysnes, Gry Hilde Nilsen, Christian Dölle, Charalampos Tzoulis
Software Mentions: 3
Published: about 4 years ago