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: VariantTools

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

Tools for Exploratory Analysis of Variant Calls
1 version
Latest release: about 1 year ago
2 dependent packages
24,362 downloads total

Papers Mentioning VariantTools 15

10.1186/s12859-016-1241-0

systemPipeR: NGS workflow and report generation environment
Cited by: 148
Author(s): Tyler W. H. Backman, Thomas Girke
Software Mentions: 19
Published: about 8 years ago

Software for Computing and Annotating Genomic Ranges
Cited by: 2,902
Author(s): Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, Marc Carlson, Robert Gentleman, Martin Morgan, Vincent J. Carey
Software Mentions: 14
Published: over 11 years ago

10.1186/s12920-020-0668-3

AMLVaran: a software approach to implement variant analysis of targeted NGS sequencing data in an oncological care setting
Cited by: 3
Author(s): Christian Wünsch, Henrik Banck, Carsten Müller‐Tidow, Martin Dugas
Software Mentions: 6
Published: almost 5 years ago

10.1186/s12863-015-0313-x

Filtering genetic variants and placing informative priors based on putative biological function
Cited by: 4
Author(s): Stefanie Friedrichs, Dörthe Malzahn, Elizabeth Pugh, Marcio Almeida, Xiao Qing Liu, Julia N. Bailey
Software Mentions: 5
Published: almost 9 years ago

10.1371/journal.ppat.1005702

Two Escape Mechanisms of Influenza A Virus to a Broadly Neutralizing Stalk-Binding Antibody
Cited by: 72
Author(s): Ningli Chai, Lee R. Swem, Mike Reichelt, Haiyin Chen-Harris, Luis Elizabeth, Summer Park, Ashley E. Fouts, P.J. Lupardus, Thomas D. Wu, Olga Li, Jacqueline McBride, Michael C. Lawrence, Min Xu, Man‐Wah Tan
Software Mentions: 4
Published: over 8 years ago

10.1186/s12859-017-1549-4

BBCAnalyzer: a visual approach to facilitate variant calling
Cited by: 0
Author(s): Sarah Sandmann, Aniek O. de Graaf, Martin Dugas
Software Mentions: 4
Published: over 7 years ago

10.3389/fimmu.2021.662443

An Integrated Genomic, Proteomic, and Immunopeptidomic Approach to Discover Treatment-Induced Neoantigens
Cited by: 17
Author(s): Niclas Olsson, Marlene L Heberling, Lichao Zhang, Suchit Jhunjhunwala, Qui Phung, Sarah Lin, Veronica G. Anania, Jennie R. Lill, Joshua E. Elias
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-019-2701-0

isma: an R package for the integrative analysis of mutations detected by multiple pipelines
Cited by: 4
Author(s): Noemi Di Nanni, Marco Moscatelli, Matteo Gnocchi, Luciano Milanesi, Ettore Mosca
Software Mentions: 3
Published: over 5 years ago

10.1002/bit.27534

Genome‐wide analysis of single nucleotide variants allows for robust and accurate assessment of clonal derivation in cell lines used to produce biologics
Cited by: 2
Author(s): Aléxandre Kuhn, Valérie Le Fourn, Igor Fisch, Nicolas Mermod
Software Mentions: 2
Published: about 4 years ago

10.1186/s12859-015-0822-7

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors
Cited by: 4
Author(s): Bart J. G. Broeckx, Frank Coopman, Geert Verhoeven, Tim Bosmans, Ingrid Gielen, Walter Dingemanse, Jimmy Saunders, Dieter Deforce, Filip Van Nieuwerburgh
Software Mentions: 2
Published: about 9 years ago

10.3390/cancers11111725

Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology
Cited by: 22
Author(s): Áron Bartha, Balázs Győrffy
Software Mentions: 2
Published: about 5 years ago

10.1038/s41418-019-0310-0

Therapeutic resistance and susceptibility is shaped by cooperative multi-compartment tumor adaptation
Cited by: 23
Author(s): Jason E. Long, Matthew J. Wongchenko, Dorothee Nickles, Wei-Jen Chung, Bu-Er Wang, Johannes Riegler, Ji Li, Qingling Li, Wendy Sandoval, Jeff Eastham-Anderson, Zora Modrušan, Teemu T. Junttila, Richard A.D. Carano, Oded Foreman, Yibing Yan, Melissa R. Junttila
Software Mentions: 2
Published: over 5 years ago

10.1186/s12864-015-2291-9

Complex regulation of ADAR-mediated RNA-editing across tissues
Cited by: 61
Author(s): Melanie A. Huntley, Melanie Lou, Leonard D. Goldstein, Michael C. Lawrence, Gerrit J.P. Dijkgraaf, Joshua S. Kaminker, Robert Gentleman
Software Mentions: 2
Published: almost 9 years ago

10.1002/mds.26845

Detection of genomic rearrangements from targeted resequencing data in Parkinson's disease patients
Cited by: 19
Author(s): Nino Spataro, Ana Roca-Umbert, Laura Cervera-Carles, Mònica Vallès, Roger Anglada, Javier Pagonabarraga, Berta Pascual-Sedano, Antònia Campolongo, Jaime Kulisevsky, Ferrán Casals, Jordi Clarimón, Elena Bosch
Software Mentions: 1
Published: about 8 years ago

10.1186/s12885-019-5622-4

Genomic profiling in ovarian cancer retreated with platinum based chemotherapy presented homologous recombination deficiency and copy number imbalances of CCNE1 and RB1 genes
Cited by: 19
Author(s): Alexandre André Balieiro Anastácio da Costa, Luísa Matos do Canto, Simon J. Larsen, Adriana Regina G. Ribeiro, Carlos Stecca, Annabeth Høgh Petersen, Mads M. Aagaard, Louise De Brot, Jan Baumbach, Glauco Baiocchi, Maria Isabel Achatz, Sílvia Regina Rogatto
Software Mentions: 1
Published: over 5 years ago