pypi: wget | Projects | Ecosyste.ms: Papers

10.12688/f1000research.27268.1

rANOMALY: AmplicoN wOrkflow for Microbial community AnaLYsis
Cited by: 16
Author(s): Sébastien Theil, Étienne Rifa
Software Mentions: 16
Published: almost 4 years ago

10.12688/f1000research.15140.2

Recommendations for the packaging and containerizing of bioinformatics software
Cited by: 32
Author(s): Bjoern Gruening, Olivier Sallou, Pablo Moreno, Felipe da Veiga Leprevost, Hervé Ménager, Dan Søndergaard, Hannes L. Röst, Timo Sachsenberg, Brian D. O’Connor, Fábio Madeira, Victoria Domínguez Del Angel, Michael R. Crusoe, Susheel Varma, Daniel Blankenberg, Rafael C. Jiménez, BioContainers Community, Yasset Perez‐Riverol
Software Mentions: 14
Published: almost 6 years ago

10.1186/s40168-019-0658-x

Sunbeam: an extensible pipeline for analyzing metagenomic sequencing experiments
Cited by: 124
Author(s): Erik L. Clarke, Louis J. Taylor, Chunyu Zhao, Andrew Jesse Connell, Jung‐Jin Lee, Bryton Fett, Frederic D. Bushman, Kyle Bittinger
Software Mentions: 11
Published: almost 6 years ago

10.1371/journal.pbio.3001365

PhyloFisher: A phylogenomic package for resolving eukaryotic relationships
Cited by: 34
Author(s): Alexander K. Tice, David Žihala, Tomáš Pánek, Robert E. Jones, Eric D. Salomaki, Serafim Nenarokov, Fabien Burki, Marek Eliáš, Laura Eme, Andrew J. Roger, Antonis Rokas, Xing‐Xing Shen, Jürgen F. H. Strassert, Martin Kolísko, Matthew W. Brown
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008748

A versatile workflow to integrate RNA-seq genomic and transcriptomic data into mechanistic models of signaling pathways
Cited by: 6
Author(s): Martín Garrido‐Rodriguez, Daniel López-López, Francisco Ortuño, María Peña‐Chilet, Eduardo Muñóz, Marco A. Calzado, Joaquı́n Dopazo
Software Mentions: 8
Published: almost 4 years ago

10.1099/mgen.0.000168

Correlation between bacterial G+C content, genome size and the G+C content of associated plasmids and bacteriophages
Cited by: 73
Author(s): Apostolos Almpanis, Martin Swain, Derek Gatherer, Neil McEwan
Software Mentions: 8
Published: almost 7 years ago

10.7717/peerj.5853

BioInstaller: a comprehensive R package to construct interactive and reproducible biological data analysis applications based on the R platform
Cited by: 3
Author(s): Jianfeng Li, Bowen Cui, Yuting Dai, Lijun Bai, Huang Jy
Software Mentions: 7
Published: about 6 years ago

10.1007/s10278-018-0080-0

Towards Portable Large-Scale Image Processing with High-Performance Computing
Cited by: 24
Author(s): Yuankai Huo, Justin A. Blaber, Stephen Damon, Brian D. Boyd, Shunxing Bao, Prasanna Parvathaneni, Camilo Bermudez Noguera, Shikha Chaganti, Vishwesh Nath, Jasmine M. Greer, Ilwoo Lyu, William R. French, Allen T. Newton, Baxter P. Rogers, Bennett A. Landman
Software Mentions: 6
Published: over 6 years ago

10.1186/1471-2105-12-S15-S5

Data hosting infrastructure for primary biodiversity data
Cited by: 13
Author(s): Anthony Goddard, Nevin Wilson, Phil Cryer, Grant Yamashita
Software Mentions: 5
Published: about 13 years ago

10.1186/1471-2164-10-22

BioMart – biological queries made easy
Cited by: 718
Author(s): Damian Smedley, Syed Haider, Benoît Ballester, Richard Holland, Darin London, Guðmundur Á. Þórisson, Arek Kasprzyk
Software Mentions: 5
Published: almost 16 years ago

10.1371/journal.pcbi.1004668

A Quick Introduction to Version Control with Git and GitHub
Cited by: 97
Author(s): John Blischak, Emily Davenport, Gregory V. Wilson
Software Mentions: 5
Published: almost 9 years ago

10.1093/gigascience/giy016

Boutiques: a flexible framework to integrate command-line applications in computing platforms
Cited by: 33
Author(s): Tristan Glatard, Gregory Kiar, Tristan Aumentado-Armstrong, Natacha Beck, Pierre Bellec, R. Bernard, Axel Bonnet, Shawn T. Brown, Sorina Camarasu-Pop, Frédéric Cervenansky, Samir Das, Rafael Ferreira da Silva, Guillaume Flandin, Pascal Girard, Krzysztof J. Gorgolewski, Charles R.G. Guttmann, Valérie Hayot‐Sasson, Pierre-Olivier Quirion, Pierre Rioux, Marc-Étienne Rousseau, Alan C. Evans
Software Mentions: 5
Published: almost 7 years ago

10.3390/ijerph16111981

Development of a WebGIS-Based Analysis Tool for Human Health Protection from the Impacts of Prescribed Fire Smoke in Southeastern USA
Cited by: 7
Author(s): Yongtao Hu, Ha Ai, M. Talat Odman, A. Vaidyanathan, Armistead G. Russell
Software Mentions: 4
Published: over 5 years ago

10.1093/bioinformatics/btaa950

RepeatFS: a file system providing reproducibility through provenance and automation
Cited by: 0
Author(s): Anthony Westbrook, Elizabeth Varki, W. Kelley Thomas
Software Mentions: 4
Published: about 4 years ago

10.7717/peerj-cs.144

The Modern Research Data Portal: a design pattern for networked, data-intensive science
Cited by: 24
Author(s): Kyle Chard, Eli Dart, Ian Foster, David J. Shifflett, Steven Tuecke, Jason Williams
Software Mentions: 4
Published: almost 7 years ago

10.1371/journal.pbio.3000333

Challenges and recommendations to improve the installability and archival stability of omics computational tools
Cited by: 53
Author(s): Serghei Mangul, Thiago Mosqueiro, Richard J. Abdill, Dat Duong, Keith Mitchell, Varuni Sarwal, Brian Hill, Jaqueline J. Brito, Russell Littman, Benjamin Statz, Angela Ka Mei Lam, Gargi Dayama, Laura Grieneisen, Lana S. Martin, Jonathan Flint, Eleazar Eskin, Ran Blekhman
Software Mentions: 4
Published: over 5 years ago

10.12688/f1000research.18676.1

pysradb: A Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive
Cited by: 23
Author(s): Saket Choudhary
Software Mentions: 4
Published: over 5 years ago

10.3389/fdata.2021.582468

Named Data Networking for Genomics Data Management and Integrated Workflows
Cited by: 3
Author(s): Cameron Ogle, David Reddick, Coleman B. McKnight, Tyler D. Biggs, Rini Pauly, Stephen P. Ficklin, F. Alex Feltus, Susmit Shannigrahi
Software Mentions: 4
Published: almost 4 years ago

10.3389/frobt.2018.00067

Oncilla Robot: A Versatile Open-Source Quadruped Research Robot With Compliant Pantograph Legs
Cited by: 32
Author(s): Alexander Spröwitz, Alexandre Tuleu, Mostafa Ajallooeian, Massimo Vespignani, Rico Möckel, P. Eckert, Michiel D’Haene, Jonas Degrave, Arne Nordmann, Benjamin Schrauwen, Jochen J. Steil, Auke Jan Ijspeert
Software Mentions: 4
Published: over 6 years ago

10.1186/s12864-019-5803-1

Expression dynamics of repetitive DNA in early human embryonic development
Cited by: 31
Author(s): Cihangir Yandım, Gökhan Karakülah
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2164-15-148

Improving transcriptome construction in non-model organisms: integrating manual and automated gene definition in Emiliania huxleyi
Cited by: 30
Author(s): Ester Feldmesser, Shilo Rosenwasser, Assaf Vardi, Shifra Ben‐Dor
Software Mentions: 3
Published: almost 11 years ago

10.7150/jgen.38516

Draft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals
Cited by: 0
Author(s): Tomoya Tsukimi, Tsubasa Watabe, Kazuki Tanaka, Mitsuhiko Sato, Haruo Suzuki, Masaru Tomita, Shinji Fukuda
Software Mentions: 3
Published: almost 5 years ago

10.3389/fgene.2019.00659

Genome-Wide Comparative Analysis of HIF Binding Sites in Cyprinus Carpio for In Silico Identification of Functional Hypoxia Response Elements
Cited by: 8
Author(s): Iliyas Rashid, Ajey Kumar Pathak, Ravindra Kumar, Prachi Srivastava, Mahender Singh, S. Murali, Basdeo Kushwaha
Software Mentions: 3
Published: over 5 years ago

10.1186/1471-2105-14-S14-S5

A cross disciplinary study of link decay and the effectiveness of mitigation techniques
Cited by: 29
Author(s): Jason Hennessey, Xijin Ge
Software Mentions: 3
Published: about 11 years ago

10.1093/molbev/msab246

Recovery of Deleted Deep Sequencing Data Sheds More Light on the Early Wuhan SARS-CoV-2 Epidemic
Cited by: 21
Author(s): Jesse D. Bloom
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-90799-y

KAUST Metagenomic Analysis Platform (KMAP), enabling access to massive analytics of re-annotated metagenomic data
Cited by: 1
Author(s): Intikhab Álam, Allan Kamau, David Kamanda Ngugi, Takashi Gojobori, Carlos M. Duarte, Vladimir B. Bajić
Software Mentions: 3
Published: over 3 years ago

10.1007/s10822-019-00236-6

Electrostatic-field and surface-shape similarity for virtual screening and pose prediction
Cited by: 23
Author(s): Ann E. Cleves, Stephen R. Johnson, Ajay N. Jain
Software Mentions: 3
Published: about 5 years ago

10.1107/S1600576716014965

<i>ContaMiner</i> and ContaBase: a webserver and database for early identification of unwantedly crystallized protein contaminants
Cited by: 25
Author(s): Arnaud Hungler, Afaque Ahmad Imtiyaz Momin, Kay Diederichs, Stefan T. Arold
Software Mentions: 2
Published: about 8 years ago

10.5808/GI.2019.17.2.e21

Improving spaCy dependency annotation and PoS tagging web service using independent NER services
Cited by: 8
Author(s): Nicola Colic, Fabio Rinaldi
Software Mentions: 2
Published: over 5 years ago

10.1093/gigascience/giw011

The Healthy Brain Network Serial Scanning Initiative: a resource for evaluating inter-individual differences and their reliabilities across scan conditions and sessions
Cited by: 64
Author(s): David O’Connor, Natan Vega Potler, Meagan Kovacs, Ting Xu, Lei Ai, John Pellman, Tamara Vanderwal, Lucas C. Parra, Saul B. Cohen, Samik Ghosh, Jasmine Escalera, Natalie Grant-Villegas, Yael Osman, Anastasia Bui, R. Cameron Craddock, Michael P. Milham
Software Mentions: 2
Published: almost 8 years ago

10.1007/s10822-017-0042-5

Molden 2.0: quantum chemistry meets proteins
Cited by: 98
Author(s): Gijs Schaftenaar, Elias Vlieg, Gert Vriend
Software Mentions: 2
Published: over 7 years ago

10.1371/journal.pone.0020409

Natural Images from the Birthplace of the Human Eye
Cited by: 85
Author(s): Gašper Tkačik, Patrick Garrigan, Charles P. Ratliff, Grega Milčinski, Jennifer M. Klein, Lucia H. Seyfarth, Peter Sterling, David H. Brainard, Vijay Balasubramanian
Software Mentions: 1
Published: over 13 years ago

10.1093/database/baaa061

LAMP2: a major update of the database linking antimicrobial peptides
Cited by: 42
Author(s): Guizi Ye, Haifeng Wu, Jinjiang Huang, Wei Wang, Kuikui Ge, Guodong Li, Jiang Zhong, Qingshan Huang
Software Mentions: 1
Published: almost 5 years ago

10.12688/f1000research.2-244.v2

Mapping whole genome shotgun sequence and variant calling in mammalian species without their reference genomes
Cited by: 7
Author(s): Theodore S. Kalbfleisch, Michael P. Heaton
Software Mentions: 1
Published: almost 11 years ago

10.1534/g3.119.400771

Challenges and Approaches to Genotyping Repetitive DNA
Cited by: 14
Author(s): Elizabeth A. Morton, Ashley N. Hall, Elizabeth Kwan, Calvin Mok, Konstantin Queitsch, Vivek Nandakumar, J Stamatoyannopoulos, Bonita J. Brewer, Robert H. Waterston, Christine Queitsch
Software Mentions: 1
Published: almost 5 years ago

10.1093/gigascience/giz077

A collection of yeast cellular electron cryotomography data
Cited by: 8
Author(s): Lu Gan, Cai Tong Ng, Chen Chen, Shujun Cai
Software Mentions: 1
Published: over 5 years ago

10.1007/s10822-017-0015-8

ForceGen 3D structure and conformer generation: from small lead-like molecules to macrocyclic drugs
Cited by: 44
Author(s): Ann E. Cleves, Ajay N. Jain
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-017-1844-0

VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences
Cited by: 14
Author(s): Duo Xu, Yousef Jaber, Pavlos Pavlidis, Ömer Gökçümen
Software Mentions: 1
Published: over 7 years ago

10.1038/sdata.2017.120

Comprehensive analyses of somatic TP53 mutation in tumors with variable mutant allele frequency
Cited by: 9
Author(s): Alexander J. Cole, Ying Zhu, Trisha Dwight, Bing Yu, Kristie A. Dickson, Gregory B. Gard, Jayne Maidens, Susan Valmadre, Anthony J. Gill, Roderick Clifton‐Bligh, Deborah J. Marsh
Software Mentions: 1
Published: over 7 years ago

10.1038/s41598-020-59165-2

PlantPepDB: A manually curated plant peptide database
Cited by: 52
Author(s): Durdam Das, Mohini Jaiswal, Fatima Nazish Khan, Shahzaib Ahamad, Shailesh Kumar
Software Mentions: 1
Published: almost 5 years ago

10.1093/molbev/mst272

Phylogenomic Test of the Hypotheses for the Evolutionary Origin of Eukaryotes
Cited by: 67
Author(s): Nicolas C. Rochette, Céline Brochier-Armanet, Manolo Gouy
Software Mentions: 1
Published: almost 11 years ago

10.1371/journal.pone.0143166

Machine Learning: How Much Does It Tell about Protein Folding Rates?
Cited by: 15
Author(s): Marc Corrales, Pol Cuscó, Dinara R. Usmanova, Heng‐Chang Chen, Natalya S. Bogatyreva, Guillaume J. Filion, Dmitry N. Ivankov
Software Mentions: 1
Published: about 9 years ago

10.1371/journal.pone.0220929

A research-based gene panel to investigate breast, ovarian and prostate cancer genetic risk
Cited by: 5
Author(s): Madison R. Bishop, Anna L. W. Huskey, John Hetzel, Nancy D. Merner
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: wget

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