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: SGSeq

https://packages.ecosyste.ms/registries/bioconductor.org/packages/SGSeq

Splice event prediction and quantification from RNA-seq data
1 version
Latest release: 10 months ago
2 dependent packages
38,013 downloads total

Papers Mentioning SGSeq 14

Divergent neuronal DNA methylation patterns across human cortical development reveal critical periods and a unique role of CpH methylation
Cited by: 65
Author(s): Amanda J. Price, Leonardo Collado‐Torres, Н. А. Иванов, Wei Xia, Emily E. Burke, Joo Heon Shin, Ran Tao, Liang Ma, Yankai Jia, Thomas M. Hyde, Joel E. Kleinman, Daniel R. Weinberger, Andrew E. Jaffe
Software Mentions: 18
Published: almost 5 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: almost 6 years ago

10.1186/s12920-017-0274-1

Quantitative analysis of cryptic splicing associated with TDP-43 depletion
Cited by: 74
Author(s): Jack Humphrey, Warren Emmett, Pietro Fratta, Adrian M. Isaacs, Vincent Plagnol
Software Mentions: 14
Published: about 7 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: over 7 years ago

10.1371/journal.ppat.1008653

Genome-wide transcriptomics identifies an early preclinical signature of prion infection
Cited by: 39
Author(s): Silvia Sorce, Mario Nuvolone, Giancarlo Russo, Andra Chincisan, Daniel Heinzer, Merve Avar, Manuela Pfammatter, Petra Schwarz, Mirzet Delic, Mattia Müller, Simone Hornemann, Despina Sanoudou, Claudia Scheckel, Adriano Aguzzi
Software Mentions: 14
Published: about 4 years ago

10.1038/s41598-021-89938-2

Improved methods for RNAseq-based alternative splicing analysis
Cited by: 20
Author(s): Rebecca F. Halperin, Apurva M. Hegde, Jessica D. Lang, Elizabeth A. Raupach, Christophe Legendre, Winnie S. Liang, Patricia LoRusso, Aleksandar Sekulić, Jeffrey A. Sosman, Jeffrey M. Trent, Sampathkumar Rangasamy, Patrick Pirrotte, Nicholas J. Schork
Software Mentions: 6
Published: about 3 years ago

10.15252/embr.202051289

LncRNA <i>Ctcflos</i> orchestrates transcription and alternative splicing in thermogenic adipogenesis
Cited by: 16
Author(s): Andrea Bast‐Habersbrunner, Christoph Kiefer, Peter Weber, Tobias Fromme, Anna Schießl, Petra Schwalie, Bart Deplancke, Yongguo Li, Martin Klingenspor
Software Mentions: 6
Published: about 3 years ago

10.1186/s12864-018-5082-2

Comparison of RNA-seq and microarray platforms for splice event detection using a cross-platform algorithm
Cited by: 17
Author(s): Juan Pablo Romero, María Ortiz-Estévez, Ander Muniategui, Soraya Carrancio, Fernando J. de Miguel, Fernando Carazo, Luis M. Montuenga, Remco Loos, Rubén Pı́o, Matthew Trotter, Ángel Rubio
Software Mentions: 5
Published: almost 6 years ago

10.1016/j.cell.2020.04.014

Evidence That STK19 Is Not an NRAS-dependent Melanoma Driver
Cited by: 12
Author(s): Marta Rodríguez‐Martínez, Thierry Boissiére, Melvin Noé González, Kevin Litchfield, Richard Mitter, Jane Walker, Svend Kjœr, Mohamed Ismail, Julian Downward, Charles Swanton, Jesper Q. Svejstrup
Software Mentions: 3
Published: about 4 years ago

10.1186/s12862-021-01833-6

The divergence of alternative splicing between ohnologs in teleost fishes
Cited by: 2
Author(s): Yuwei Wang, Baocheng Guo
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0156132

Prediction and Quantification of Splice Events from RNA-Seq Data
Cited by: 93
Author(s): Leonard D. Goldstein, Yi Cao, Grégoire Pau, Michael Lawrence, Thomas D. Wu, Somasekar Seshagiri, Robert Gentleman
Software Mentions: 2
Published: about 8 years ago

10.15252/embj.201798684

Mice with endogenous <scp>TDP</scp> ‐43 mutations exhibit gain of splicing function and characteristics of amyotrophic lateral sclerosis
Cited by: 116
Author(s): Pietro Fratta, Prasanth Sivakumar, Jack Humphrey, Kitty Lo, Thomas C. Ricketts, Hugo M De Oliveira, José M. Brito-Armas, Bernadett Kalmár, Agnieszka M Ule, Yichao Yu, Nicol Birsa, Cristian Bodo, Toby Collins, Alexander E. Conicella, Alan Mejia Maza, Alessandro Marrero‐Gagliardi, Michelle Stewart, Joffrey Mianné, Silvia Corrochano, Warren Emmett, Gemma Codner, Michael J. Groves, Ryutaro Fukumura, Yoichi Gondo, Mark F. Lythgoe, Erwin Pauws, Emma Peskett, Philip Stanier, Lydia Teboul, Martina Hallegger, Andrea Calvo, Adriano Chiò, Adrian M. Isaacs, Nicolas L. Fawzi, Eric Wang, David E. Housman, Francisco E. Baralle, Linda Greensmith, Emanuele Buratti, Vincent Plagnol, Elizabeth Fisher, Abraham Acevedo‐Arozena
Software Mentions: 2
Published: about 6 years ago

10.1038/s41598-018-27951-8

Next generation sequencing identifies novel disease-associated BEST1 mutations in Bestrophinopathy patients
Cited by: 9
Author(s): Thong Tien Nguyen, B Poornachandra, Anshuman Verma, Ruchir Mehta, Sameer Phalke, Rajani Battu, Vedam Ramprasad, Andrew S. Peterson, Arkasubhra Ghosh, Somasekar Seshagiri
Software Mentions: 1
Published: about 6 years ago

10.18632/oncotarget.14076

Characterization of RNA editome in primary and metastatic lung adenocarcinomas
Cited by: 6
Author(s): Lihua Peng, Leo J. Lee, Heng Xiong, Hong Su, Jun-Hua Rao, Dakai Xiao, Jianxing He, Kui Wu, Dongbing Liu
Software Mentions: 1
Published: over 7 years ago