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: cran: optparse

https://packages.ecosyste.ms/registries/cran.r-project.org/packages/optparse

Command Line Option Parser
19 versions
Latest release: over 2 years ago
10 dependent packages
28,384 downloads last month

Papers Mentioning optparse 15

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking
Cited by: 64
Author(s): Charalampos Lazaris, Stephen M. Kelly, Panagiotis Ntziachristos, Iannis Aifantis, Aristotelis Tsirigos
Software Mentions: 28
Published: almost 8 years ago

10.1371/journal.pgen.1008927

On the cross-population generalizability of gene expression prediction models
Cited by: 34
Author(s): Kevin L. Keys, Angel C. Y. Mak, Marquitta J. White, Walter L. Eckalbar, Andrew Dahl, Joel Mefford, Anna V. Mikhaylova, María G. Contreras, Jennifer R. Elhawary, Celeste Eng, Donglei Hu, Scott Huntsman, Sam S. Oh, Sandra Salazar, Michael A. LeNoir, Jimmie C. Ye, Timothy A. Thornton, Noah Zaitlen, Esteban G. Burchard, Christopher R. Gignoux
Software Mentions: 16
Published: over 4 years ago

10.1186/s12859-020-03860-4

Finding a suitable library size to call variants in RNA-Seq
Cited by: 3
Author(s): Anna Quaglieri, Christoffer Flensburg, Terence P. Speed, Ian J. Majewski
Software Mentions: 15
Published: almost 4 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: over 7 years ago

10.1371/journal.pone.0244005

DDRP: Real-time phenology and climatic suitability modeling of invasive insects
Cited by: 13
Author(s): Brittany S. Barker, Leonard B. Coop, Tyson Wepprich, Fritzi S. Grevstad, Gericke Cook
Software Mentions: 12
Published: almost 4 years ago

10.1186/s12859-020-3475-0

PACVr: plastome assembly coverage visualization in R
Cited by: 184
Author(s): Michael Gruenstaeudl, Nils Jenke
Software Mentions: 9
Published: over 4 years ago

10.3389/fmicb.2018.01323

Exposure to Arsenic Alters the Microbiome of Larval Zebrafish
Cited by: 37
Author(s): Dylan Dahan, Brooke A. Jude, Regina Lamendella, Felicia Keesing, Gabriel G. Perron
Software Mentions: 9
Published: over 6 years ago

10.1007/s12275-020-9536-2

STATR: A simple analysis pipeline of Ribo-Seq in bacteria
Cited by: 7
Author(s): Donghui Choe, Bernhard Ø. Palsson, Byung-Kwan Cho
Software Mentions: 6
Published: almost 5 years ago

10.1371/journal.pgen.1006667

Elucidation of the calcineurin-Crz1 stress response transcriptional network in the human fungal pathogen Cryptococcus neoformans
Cited by: 85
Author(s): Eve W. L. Chow, Shelly Applen Clancey, R. Blake Billmyre, Anna Floyd Averette, Joshua A. Granek, Piotr A. Mieczkowski, María E. Cárdenas, Joseph Heitman
Software Mentions: 5
Published: over 7 years ago

10.1186/s12866-020-01845-0

Impacts of a novel defensive symbiosis on the nematode host microbiome
Cited by: 7
Author(s): Dylan Dahan, Gail Preston, Jordan E. Sealey, Kayla C. King
Software Mentions: 5
Published: over 4 years ago

10.3389/fmicb.2020.00125

Gut Microbiota Plasticity Influences the Adaptability of Wild and Domestic Animals in Co-inhabited Areas
Cited by: 15
Author(s): Wen Qin, Pengfei Song, Gonghua Lin, YanGan Huang, Lei Wang, Xiaowen Zhou, Shengqing Li, Tongzuo Zhang
Software Mentions: 5
Published: almost 5 years ago

10.1093/ije/dyx204

Software Application Profile: PHESANT: a tool for performing automated phenome scans in UK Biobank
Cited by: 138
Author(s): Louise A C Millard, Neil M Davies, Tom R. Gaunt, George Davey Smith, Kate Tilling
Software Mentions: 5
Published: about 7 years ago

10.1186/s12859-015-0644-7

SuRankCo: supervised ranking of contigs in de novo assemblies
Cited by: 13
Author(s): Mathias Kuhring, Piotr Wojtek Dabrowski, Vitor C. Piro, Andreas Nitsche, Bernhard Y. Renard
Software Mentions: 4
Published: over 9 years ago

10.1186/s12859-020-03601-7

AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids
Cited by: 0
Author(s): Alexander Coulton, Keith J. Edwards
Software Mentions: 4
Published: over 4 years ago

10.1093/ije/dyaa004

GLU: a software package for analysing continuously measured glucose levels in epidemiology
Cited by: 12
Author(s): Louise A C Millard, Nashita Patel, Kate Tilling, Melanie Lewcock, Peter A. Flach, Debbie A. Lawlor
Software Mentions: 4
Published: almost 5 years ago