cran: SimSeq | Projects | Ecosyste.ms: Papers

10.3390/life11070716

Single-Cell Transcriptome Profiling Simulation Reveals the Impact of Sequencing Parameters and Algorithms on Clustering
Cited by: 0
Author(s): Yunhe Liu, Aoshen Wu, Xueqing Peng, Xiaona Liu, Gang Liu, Lei Liu
Software Mentions: 15
Published: over 3 years ago

10.1016/j.csbj.2015.08.004

Dynamics in Transcriptomics: Advancements in RNA-seq Time Course and Downstream Analysis
Cited by: 73
Author(s): Daniel Spies, Constance Ciaudo
Software Mentions: 11
Published: almost 10 years ago

10.1186/s13059-018-1466-5

Differential gene expression analysis tools exhibit substandard performance for long non-coding RNA-sequencing data
Cited by: 40
Author(s): Alemu Takele Assefa, Katrijn De Paepe, Celine Everaert, Pieter Mestdagh, Olivier Thas, Jo Vandesompele
Software Mentions: 10
Published: over 6 years ago

10.1186/1756-0500-7-68

Simulating a population genomics data set using FlowSim
Cited by: 2
Author(s): Ketil Malde
Software Mentions: 6
Published: almost 11 years ago

10.1186/s13015-019-0137-8

SNPs detection by eBWT positional clustering
Cited by: 24
Author(s): Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone
Software Mentions: 5
Published: almost 6 years ago

10.1093/gigascience/giz045

A multi-omics data simulator for complex disease studies and its application to evaluate multi-omics data analysis methods for disease classification
Cited by: 24
Author(s): Ren‐Hua Chung, Chen-Yu Kang
Software Mentions: 4
Published: over 5 years ago

10.1371/journal.pone.0049110

Generation of Artificial FASTQ Files to Evaluate the Performance of Next-Generation Sequencing Pipelines
Cited by: 48
Author(s): Matthew Frampton, Richard S. Houlston
Software Mentions: 4
Published: about 12 years ago

10.1186/s12859-020-3450-9

Data-based RNA-seq simulations by binomial thinning
Cited by: 19
Author(s): David Gerard
Software Mentions: 4
Published: over 4 years ago

10.1371/journal.pone.0187287

EAMA: Empirically adjusted meta-analysis for large-scale simultaneous hypothesis testing in genomic experiments
Cited by: 3
Author(s): Sinjini Sikdar, Somnath Datta, Susmita Datta
Software Mentions: 4
Published: about 7 years ago

10.1128/mSphere.00786-20

A Genome Epidemiological Study of SARS-CoV-2 Introduction into Japan
Cited by: 39
Author(s): Tsuyoshi Sekizuka, Kentaro Itokawa, Masanori Hashino, Tetsuro Kawano-Sugaya, Rina Tanaka, Koji Yatsu, Asami Ohnishi, Keiko Goto, Hiroyuki Tsukagoshi, Hayato Ehara, Kenji Sadamasu, Masakatsu Taira, Shuzo Shibata, Ryohei Nomoto, Satoshi Hiroi, Miho Toho, Tomoe Shimada, Takeshi Matsui, Tomimasa Sunagawa, Hajime Kamiya, Yuichiro Yahata, Takashi Yamagishi, Motoi Suzuki, Takaji Wakita, Makoto Kuroda
Software Mentions: 3
Published: almost 4 years ago

10.1186/1471-2105-13-S14-S8

GapFiller: a de novo assembly approach to fill the gap within paired reads
Cited by: 281
Author(s): Francesca Nadalin, Francesco Vezzi, Alberto Policriti
Software Mentions: 3
Published: about 12 years ago

10.1186/s12859-017-1760-3

CLOVE: classification of genomic fusions into structural variation events
Cited by: 7
Author(s): Jan Schröder, Adrianto Wirawan, Bertil Schmidt, Anthony T. Papenfuss
Software Mentions: 3
Published: over 7 years ago

10.1186/s12859-020-03586-3

Variable-order reference-free variant discovery with the Burrows-Wheeler Transform
Cited by: 8
Author(s): Nicola Prezza, Nadia Pisanti, Marinella Sciortino, Giovanna Rosone
Software Mentions: 3
Published: about 4 years ago

10.1186/1471-2164-13-74

GemSIM: general, error-model based simulator of next-generation sequencing data
Cited by: 141
Author(s): Kerensa McElroy, Fabio Luciani, Torsten Thomas
Software Mentions: 3
Published: almost 13 years ago

10.1186/s12864-016-2463-2

Improvement in detection of minor alleles in next generation sequencing by base quality recalibration
Cited by: 7
Author(s): Shengyu Ni, Mark Stoneking
Software Mentions: 3
Published: over 8 years ago

10.1186/s13100-018-0143-2

Retrophylogenomics in rorquals indicate large ancestral population sizes and a rapid radiation
Cited by: 17
Author(s): Fritjof Lammers, Moritz Blumer, Cornelia Rücklé, Maria A. Nilsson
Software Mentions: 3
Published: almost 6 years ago

10.1371/journal.pone.0060058

Identifying and Classifying Trait Linked Polymorphisms in Non-Reference Species by Walking Coloured de Bruijn Graphs
Cited by: 26
Author(s): Richard M. Leggett, Ricardo H. Ramírez-González, Walter Verweij, Cintia Goulart Kawashima, Zamin Iqbal, Jonathan D. G. Jones, Mario Cáccamo, Dan MacLean
Software Mentions: 3
Published: over 11 years ago

10.1371/journal.pone.0125201

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data
Cited by: 55
Author(s): Lilit Nersisyan, Arsen Arakelyan
Software Mentions: 3
Published: over 9 years ago

10.1371/journal.ppat.1006882

AIG1 affects in vitro and in vivo virulence in clinical isolates of Entamoeba histolytica
Cited by: 25
Author(s): Kumiko Nakada‐Tsukui, Tsuyoshi Sekizuka, Emi Sato-Ebine, Aleyla Escueta-de Cadiz, Dar-Der Ji, Kentaro Tomii, Makoto Kuroda, Tomoyoshi Nozaki
Software Mentions: 2
Published: over 6 years ago

10.1186/1471-2164-14-S1-S12

Unraveling overlapping deletions by agglomerative clustering
Cited by: 5
Author(s): Roland Wittler
Software Mentions: 2
Published: almost 12 years ago

10.1186/s12859-015-0801-z

An investigation of causes of false positive single nucleotide polymorphisms using simulated reads from a small eukaryote genome
Cited by: 32
Author(s): Antonio Ribeiro, Agnieszka A. Golicz, Christine A. Hackett, Iain Milne, Gordon Stephen, David Marshall, Andrew J. Flavell, Micha Bayer
Software Mentions: 2
Published: about 9 years ago

10.1186/s12859-016-0910-3

Fast, accurate, and lightweight analysis of BS-treated reads with ERNE 2
Cited by: 11
Author(s): Nicola Prezza, Francesco Vezzi, Max Käller, Alberto Policriti
Software Mentions: 2
Published: almost 9 years ago

10.1371/journal.pone.0131933

Direct Gamete Sequencing Reveals No Evidence for Segregation Distortion in House Mouse Hybrids
Cited by: 10
Author(s): Russell Corbett-Detig, Emily Jacobs-Palmer, Daniel L. Hartl, Hopi E. Hoekstra
Software Mentions: 1
Published: over 9 years ago

10.1186/1471-2105-13-S6-S7

PAIR: polymorphic Alu insertion recognition
Cited by: 6
Author(s): Jón Ingi Sveinbjörnsson, Bjarni V. Halldórsson
Software Mentions: 1
Published: over 12 years ago

10.1186/s12864-020-06982-4

Using earth mover’s distance for viral outbreak investigations
Cited by: 10
Author(s): Andrew Melnyk, S. P. Knyazev, Fredrik Vannberg, Leonid Bunimovich, Pavel Skums, Alexander Zelikovsky
Software Mentions: 1
Published: almost 4 years ago

10.1371/journal.pone.0189710

AMYCNE: Confident copy number assessment using whole genome sequencing data
Cited by: 19
Author(s): Jesper Eisfeldt, Daniel Nilsson, Johanna C. Andersson‐Assarsson, Anna Wedell
Software Mentions: 1
Published: over 6 years ago

10.1371/journal.pone.0114848

Complete Genome Sequence and Comparative Genomic Analysis of Mycobacterium massiliense JCM 15300 in the Mycobacterium abscessus Group Reveal a Conserved Genomic Island MmGI-1 Related to Putative Lipid Metabolism
Cited by: 18
Author(s): Tsuyoshi Sekizuka, Masahiro Kai, Kazue Nakanaga, Noboru Nakata, Yuko Kazumi, Shingo Maeda, Masahiko Makino, Yoshihiko Hoshino, Makoto Kuroda
Software Mentions: 1
Published: almost 10 years ago

10.1186/1471-2105-15-S9-S14

A better sequence-read simulator program for metagenomics
Cited by: 31
Author(s): Stephen E. Johnson, Brett Trost, Jeffrey R. Long, Vanessa Pittet, Anthony Kusalik
Software Mentions: 1
Published: about 10 years ago

10.1038/ejhg.2016.147

A framework for the detection of de novo mutations in family-based sequencing data
Cited by: 26
Author(s): Laurent C. Francioli, Mircea Cretu-Stancu, Kiran Garimella, Menachem Fromer, Wigard P. Kloosterman, Kaitlin E. Samocha, Benjamin M. Neale, Mark J. Daly, Eric Banks, Mark A. DePristo, Paul Iw de Bakker
Software Mentions: 1
Published: about 8 years ago

10.1186/1471-2105-16-S9-S4

Fast randomized approximate string matching with succinct hash data structures
Cited by: 6
Author(s): Alberto Policriti, Nicola Prezza
Software Mentions: 1
Published: over 9 years ago

10.1186/s13059-020-01993-6

Varlociraptor: enhancing sensitivity and controlling false discovery rate in somatic indel discovery
Cited by: 12
Author(s): Johannes Köster, Louis Dijkstra, Tobias Marschall, Alexander Schönhuth
Software Mentions: 1
Published: over 4 years ago

10.1371/journal.pcbi.1003515

Viral Quasispecies Assembly via Maximal Clique Enumeration
Cited by: 87
Author(s): Armin Töpfer, Tobias Marschall, Rowena A. Bull, Fabio Luciani, Alexander Schönhuth, Niko Beerenwinkel
Software Mentions: 1
Published: over 10 years ago

10.7717/peerj.2997

Variant profiling of evolving prokaryotic populations
Cited by: 16
Author(s): Markus Zojer, Lisa N Schuster, Frederik Schulz, Alexander Pfundner, Matthias Horn, Thomas Rattei
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pcbi.1004229

ConPADE: Genome Assembly Ploidy Estimation from Next-Generation Sequencing Data
Cited by: 25
Author(s): Gabriel Rodrigues Alves Margarido, David Heckerman
Software Mentions: 1
Published: over 9 years ago

10.1371/journal.pntd.0005386

Comparative genome analysis of VSP-II and SNPs reveals heterogenic variation in contemporary strains of Vibrio cholerae O1 isolated from cholera patients in Kolkata, India
Cited by: 23
Author(s): Daisuke Imamura, Masatomo Morita, Tsuyoshi Sekizuka, Tamaki Mizuno, Taichiro Takemura, Tetsu Yamashiro, Goutam Chowdhury, Gururaja P. Pazhani, Asish K. Mukhopadhyay, Thandavarayan Ramamurthy, Shin Ichi Miyoshi, Makoto Kuroda, Sumió Shinoda, Makoto Ohnishi
Software Mentions: 1
Published: almost 8 years ago

10.1371/journal.pone.0031002

Feature-by-Feature – Evaluating De Novo Sequence Assembly
Cited by: 60
Author(s): Francesco Vezzi, Giuseppe Narzisi, Bud Mishra
Software Mentions: 1
Published: almost 13 years ago

Ecosyste.ms: Papers

Projects: cran: SimSeq

Papers Mentioning SimSeq 36