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: pypi: shell

https://packages.ecosyste.ms/registries/pypi.org/packages/shell

A better way to run shell commands in Python.
2 versions
Latest release: almost 11 years ago
1 dependent package
30,144 downloads last month

Papers Mentioning shell 207

10.1016/j.patter.2021.100322
The role of metadata in reproducible computational research
Cited by: 38
Author(s): Jeremy Leipzig, Daniel Nüst, Charles Tapley Hoyt, Karthik Ram, Jane Greenberg
Software Mentions: 21
Published: about 3 years ago
10.1093/gigascience/giaa026
ShinyLearner: A containerized benchmarking tool for machine-learning classification of tabular data
Cited by: 13
Author(s): Stephen R. Piccolo, Terry J. Lee, Erica Suh, Kimball T Hill
Software Mentions: 21
Published: over 4 years ago
10.1186/s12859-020-03577-4
NASQAR: a web-based platform for high-throughput sequencing data analysis and visualization
Cited by: 38
Author(s): Ayman Yousif, Nizar Drou, Jillian Rowe, Mohammed Khalfan, Kristin C. Gunsalus
Software Mentions: 17
Published: over 4 years ago
10.1038/sdata.2018.179
Computational workflow to study the seasonal variation of secondary metabolites in nine different bryophytes
Cited by: 13
Author(s): Kristian Peters, Karin Gorzolka, Helge Bruelheide, Steffen Neumann
Software Mentions: 17
Published: about 6 years ago
10.3389/fnins.2014.00067
Flexible multivariate hemodynamics fMRI data analyses and simulations with PyHRF
Cited by: 11
Author(s): Vincent Thomas, Solveig Badillo, Laurent Risser, Lotfi Chaâri, Christine Bakhous, Florence Forbes, Philippe Ciuciu
Software Mentions: 14
Published: over 10 years ago
10.12688/f1000research.8986.2
Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses
Cited by: 483
Author(s): Ben J. Callahan, Kris Sankaran, Julia Fukuyama, Paul J. McMurdie, Susan Holmes
Software Mentions: 13
Published: about 8 years ago
10.1093/database/bay027
Maser: one-stop platform for NGS big data from analysis to visualization
Cited by: 38
Author(s): Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo
Software Mentions: 10
Published: almost 7 years ago
10.3389/fmicb.2018.01598
Microbiome Composition in Both Wild-Type and Disease Model Mice Is Heavily Influenced by Mouse Facility
Cited by: 60
Author(s): Kristopher D. Parker, Shannon E. Albeke, Jason P. Gigley, Allan M. Goldstein, Naomi Ward
Software Mentions: 10
Published: over 6 years ago
10.1093/gigascience/giab062
Genetic demultiplexing of pooled single-cell RNA-sequencing samples in cancer facilitates effective experimental design
Cited by: 16
Author(s): Lukas M. Weber, Ariel A. Hippen, Peter Hickey, Kristofer C. Berrett, Jason Gertz, Jennifer A. Doherty, Casey S. Greene, Stephanie C. Hicks
Software Mentions: 8
Published: about 3 years ago
10.1093/gigascience/giy023
The Scientific Filesystem
Cited by: 1
Author(s): Vanessa Sochat
Software Mentions: 7
Published: over 6 years ago
10.2196/jmir.5144
Establishing a Link Between Prescription Drug Abuse and Illicit Online Pharmacies: Analysis of Twitter Data
Cited by: 82
Author(s): Takeo Katsuki, Tim K. Mackey, Raphael Cuomo
Software Mentions: 7
Published: almost 9 years ago
10.3389/fninf.2013.00010
The Virtual Brain: a simulator of primate brain network dynamics
Cited by: 296
Author(s): Paula Sanz-Leon, S. A. Knock, Michael Woodman, Lia Domide, Jochen Mersmann, Anthony R. McIntosh, Viktor K. Jirsa
Software Mentions: 7
Published: almost 12 years ago
10.1038/sdata.2017.44
Construction of a map-based reference genome sequence for barley, Hordeum vulgare L.
Cited by: 119
Author(s): Sebastian Beier, Axel Himmelbach, Christian Colmsee, Xiao Qi Zhang, Roberto A. Barrero, Qisen Zhang, Lin Li, Micha Bayer, Dan Bolser, Stefan Taudien, Marco Groth, Marius Felder, Alex Hastie, Hana Šimková, Helena Staňková, Jan Vrána, Saki Chan, María Muñoz‐Amatriaín, Rachid Ounit, Steve Wanamaker, Thomas Schmutzer, Lala Aliyeva-Schnorr, Stefano Grasso, Jaakko Tanskanen, Dharanya Sampath, Darren Heavens, Sujie Cao, Brett Chapman, Fei Dai, Yong Han, Hua Li, Xuan Li, Chongyun Lin, John K. McCooke, Cong Tan, Songbo Wang, Shuya Yin, Gaofeng Zhou, Jesse Poland, M. Bellgard, Andreas Houben, Jaroslav Doležel, Sarah Ayling, Stefano Lonardi, Peter Langridge, Gary J. Muehlbauer, Paul J. Kersey, Matthew D. Clark, Mario Cáccamo, Alan H. Schulman, Matthias Platzer, Timothy J. Close, Mats Hansson, Guoping Zhang, Ilka Braumann, Chengdao Li, Robbie Waugh, Uwe Scholz, Nils Stein, Martin Mascher
Software Mentions: 6
Published: over 7 years ago
10.12688/f1000research.13049.2
RSEQREP: RNA-Seq Reports, an open-source cloud-enabled framework for reproducible RNA-Seq data processing, analysis, and result reporting
Cited by: 6
Author(s): Travis L. Jensen, Michael Frasketi, Kevin P. Conway, Leigh Villarroel, Heather Hill, Konstantinos Krampis, Johannes Goll
Software Mentions: 6
Published: over 6 years ago
10.12688/f1000research.29032.2
Sustainable data analysis with Snakemake
Cited by: 502
Author(s): Felix Mölder, Kim Philipp Jablonski, Brice Letcher, Michael B. Hall, Christopher H. Tomkins-Tinch, Vanessa Sochat, Jan Förster, Soohyun Lee, Sven Twardziok, Alexander Kanitz, Andreas Wilm, Manuel Holtgrewe, Sven Rahmann, Sven Nahnsen, Johannes Köster
Software Mentions: 6
Published: over 3 years ago
10.3389/fmicb.2019.00618
Metagenomic Insights Into a Cellulose-Rich Niche Reveal Microbial Cooperation in Cellulose Degradation
Cited by: 32
Author(s): Jin-Ming Cui, Guoqin Mai, Zuowei Wang, Quan Liu, Yan Zhou, Yingfei Ma, Chenli Liu
Software Mentions: 6
Published: over 5 years ago
10.1093/gigascience/giy059
zUMIs - A fast and flexible pipeline to process RNA sequencing data with UMIs
Cited by: 244
Author(s): Swati Parekh, Christoph Ziegenhain, Beate Vieth, Wolfgang Enard, Ines Hellmann
Software Mentions: 6
Published: over 6 years ago
10.1371/journal.pone.0106397
RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
Cited by: 138
Author(s): Mehmet K. Samur
Software Mentions: 6
Published: about 10 years ago
10.7150/thno.47390
Upregulation of amplified in breast cancer 1 contributes to pancreatic ductal adenocarcinoma progression and vulnerability to blockage of hedgehog activation
Cited by: 2
Author(s): Licen Li, Jiaolin Bao, Haitao Wang, Josh Haipeng Lei, Cheng Peng, Jianming Zeng, Hao Wu, Xu Zhang, Xiaoling Xu, Chundong Yu, Chu Xia Deng, Qiang Chen
Software Mentions: 6
Published: almost 4 years ago
10.1186/s12870-014-0315-2
The chickpea genomic web resource: visualization and analysis of the desi-type Cicer arietinum nuclear genome for comparative exploration of legumes
Cited by: 8
Author(s): Gopal Misra, Piyush Priya, Nitesh Bandhiwal, Neha Bareja, Mukesh Jain, Sabhyata Bhatia, Debasis Chattopadhyay, Akhilesh K. Tyagi, Gitanjali Yadav
Software Mentions: 6
Published: almost 10 years ago
10.1186/s12859-016-1104-8
SUSHI: an exquisite recipe for fully documented, reproducible and reusable NGS data analysis
Cited by: 75
Author(s): Masaomi Hatakeyama, Lennart Opitz, Giancarlo Russo, Weihong Qi, Ralph Schlapbach, Hubert Rehrauer
Software Mentions: 6
Published: over 8 years ago
10.1093/gigascience/giaa059
Genomic consequences of dietary diversification and parallel evolution due to nectarivory in leaf-nosed bats
Cited by: 16
Author(s): Yocelyn T. Gutiérrez-Guerrero, Enrique Ibarra-Laclette, Carlos Martı́nez del Rio, Josué Barrera‐Redondo, Eria A. Rebollar, Jorge Ortega, Livia León‐Paniagua, Araxi O. Urrutia, Erika Aguirre‐Planter, Luis E. Eguiarte
Software Mentions: 6
Published: over 4 years ago
10.3390/genes9080392
RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates
Cited by: 16
Author(s): Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, Ivo L. Hofacker
Software Mentions: 6
Published: over 6 years ago
10.1186/1471-2105-13-102
Workflows for microarray data processing in the Kepler environment
Cited by: 14
Author(s): Thomas Stropp, Timothy M. McPhillips, Bertram Ludäscher, Mark Bieda
Software Mentions: 6
Published: over 12 years ago
10.1186/1751-0473-6-4
Parallel biocomputing
Cited by: 0
Author(s): Kenneth S Kompass, Thomas J. Hoffmann, John S. Witte
Software Mentions: 6
Published: over 13 years ago
10.1186/1756-0500-4-171
CloudAligner: A fast and full-featured MapReduce based tool for sequence mapping
Cited by: 101
Author(s): Tung Nguyen, Wei Shi, Douglas M. Ruden
Software Mentions: 5
Published: over 13 years ago
10.1038/s41598-017-14595-3
UClncR: Ultrafast and comprehensive long non-coding RNA detection from RNA-seq
Cited by: 27
Author(s): Zhifu Sun, Asha Nair, Xianfeng Chen, Naresh Prodduturi, Junwen Wang, Jean Pierre A. Kocher
Software Mentions: 5
Published: about 7 years ago
10.1371/journal.pcbi.1006767
The intrinsic dimension of protein sequence evolution
Cited by: 14
Author(s): Elena Facco, Andrea Pagnani, Elena Tea Russo, Alessandro Laio
Software Mentions: 5
Published: over 5 years ago
10.1093/bioinformatics/btx179
<i>Fuento</i>: functional enrichment for bioinformatics
Cited by: 5
Author(s): David Tobias Weichselbaum, Bojan Žagrović, Anton A. Polyansky
Software Mentions: 5
Published: over 7 years ago
10.1107/S0907444911049791
Conventions and workflows for using <i>Situs</i>
Cited by: 157
Author(s): Willy Wriggers
Software Mentions: 5
Published: over 12 years ago
10.1093/bioinformatics/bty181
Reactome Pengine: a web-logic API to the Homo sapiens reactome
Cited by: 6
Author(s): Samuel R Neaves, Sophia Tsoka, Louise A C Millard
Software Mentions: 5
Published: over 6 years ago
10.1038/s41598-018-27078-w
Global miRNA expression profile reveals novel molecular players in aneurysmal subarachnoid haemorrhage
Cited by: 19
Author(s): Kátia de Paiva Lopes, Tatiana Vinasco-Sandoval, Ricardo Assunção Vialle, Fernando Mendes Paschoal, Vanessa Albuquerque Paschoal Aviz Bastos, Edson Bor‐Seng‐Shu, Manoel Jacobsen Teixeira, Elizabeth Sumi Yamada, Pablo Diego do Carmo Pinto, Amanda Ferreira Vidal, André M. Ribeiro-dos-Santos, Fabiano Cordeiro Moreira, Sidney Emanuel Batista dos Santos, Eric Homero Albuquerque Paschoal, Ândrea Ribeiro‐dos‐Santos
Software Mentions: 5
Published: over 6 years ago
10.12688/f1000research.17456.1
pdb-tools: a swiss army knife for molecular structures
Cited by: 81
Author(s): João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M. J. J. Bonvin
Software Mentions: 5
Published: almost 6 years ago
10.1371/journal.pcbi.1006843
Script of Scripts: A pragmatic workflow system for daily computational research
Cited by: 11
Author(s): Gao Wang, Bo Peng
Software Mentions: 5
Published: over 5 years ago
10.1186/s12920-018-0391-5
Indel sensitive and comprehensive variant/mutation detection from RNA sequencing data for precision medicine
Cited by: 5
Author(s): Naresh Prodduturi, Aditya Bhagwate, Jean Pierre A. Kocher, Zhifu Sun
Software Mentions: 5
Published: about 6 years ago
10.1371/journal.pone.0172583
Solving global shallow water equations on heterogeneous supercomputers
Cited by: 2
Author(s): Haohuan Fu, Lin Gan, Chao Yang, Wei Xue, Lanning Wang, Xinliang Wang, Xiaomeng Huang, Guangwen Yang
Software Mentions: 5
Published: over 7 years ago
10.1038/s41598-020-66374-2
Mutations in virus-derived small RNAs
Cited by: 6
Author(s): Deepti Nigam, Katherine LaTourrette, Hernán García-Ruíz
Software Mentions: 5
Published: over 4 years ago
10.1038/srep26447
MetaTrans: an open-source pipeline for metatranscriptomics
Cited by: 84
Author(s): Xavier Martínez, Marta Pozuelo, Victoria Pascal, David Campos, Marta Gut, Fernando Azpiroz, Francisco Guarner, Chaysavanh Manichanh
Software Mentions: 5
Published: over 8 years ago
10.7717/peerj.1319
Anvi’o: an advanced analysis and visualization platform for ‘omics data
Cited by: 1,274
Author(s): A. Murat Eren, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, Tom O. Delmont
Software Mentions: 5
Published: about 9 years ago
10.1186/1471-2164-14-100
A hybrid next generation transcript sequencing-based approach to identify allelic and homeolog-specific single nucleotide polymorphisms in allotetraploid white clover
Cited by: 19
Author(s): Istvàn Nagy, Susanne Barth, Jeanne Mehenni-Ciz, Michael T. Abberton, Dan Milbourne
Software Mentions: 5
Published: almost 12 years ago
10.3389/fninf.2016.00017
BluePyOpt: Leveraging Open Source Software and Cloud Infrastructure to Optimise Model Parameters in Neuroscience
Cited by: 104
Author(s): Werner Van Geit, Michael Gevaert, Giuseppe Chindemi, Christian Rössert, Jean-Denis Courcol, Eilif Müller, Felix Schürmann, Idan Segev, Henry Markram
Software Mentions: 5
Published: over 8 years ago
10.7717/peerj-cs.606
Provenance-and machine learning-based recommendation of parameter values in scientific workflows
Cited by: 0
Author(s): Daniel Silva, Esther Pacitti, Aline Paes, Daniel de Oliveira
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pcbi.1008622
Using prototyping to choose a bioinformatics workflow management system
Cited by: 20
Author(s): Michael Jackson, Kostas Kavoussanakis, Eric Wallace
Software Mentions: 5
Published: over 3 years ago
10.1371/journal.pone.0042678
The Role of Master Regulators in the Metabolic/Transcriptional Coupling in Breast Carcinomas
Cited by: 19
Author(s): Karol Baca-López, M. Mayorga, Alfredo Hidalgo-Miranda, Nora Gutiérrez-Nájera, Enrique Hernández‐Lemus
Software Mentions: 5
Published: about 12 years ago
10.1186/s12859-019-3100-2
RACS: rapid analysis of ChIP-Seq data for contig based genomes
Cited by: 4
Author(s): Marcelo Ponce, Alejandro Saettone, Syed Nabeel‐Shah, Jeffrey Fillingham
Software Mentions: 5
Published: about 5 years ago
10.1371/journal.pcbi.1006373
Designing and running an advanced Bioinformatics and genome analyses course in Tunisia
Cited by: 6
Author(s): Fatma Z. Guerfali, Dhafer Laouini, Abdellatif Boudabous, Fredj Tekaia
Software Mentions: 5
Published: almost 6 years ago
10.3390/s120607109
Personal Pervasive Environments: Practice and Experience
Cited by: 5
Author(s): Francisco Ballesteros, Gorka Guardiola, Enrique Soriano
Software Mentions: 4
Published: over 12 years ago
10.3390/microorganisms9040841
A Primer on the Analysis of High-Throughput Sequencing Data for Detection of Plant Viruses
Cited by: 29
Author(s): Denis Kutnjak, Lucie Tamisier, Ian Adams, Neil Boonham, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Jan Kreuze, Marie Lefebvre, Gonçalo Silva, Martha Malapi‐Wight, Paolo Margaria, Irena Mavrič Pleško, Sam McGreig, Laura Miozzi, Benoît Remenant, Jean-Sébastien Reynard, Johan Rollin, M. Rott, Olivier Schumpp, Sébastien Massart, Annelies Haegeman
Software Mentions: 4
Published: over 3 years ago
10.3389/fgene.2014.00293
A bioinformatics workflow for detecting signatures of selection in genomic data
Cited by: 49
Author(s): Murray Cadzow, James Boocock, Hoang Nguyen, Phillip Wilcox, Tony R. Merriman, Michael A. Black
Software Mentions: 4
Published: about 10 years ago
10.1186/1471-2105-10-221
An introduction to scripting in Ruby for biologists
Cited by: 15
Author(s): Jan Aerts, Andy Law
Software Mentions: 4
Published: over 15 years ago
10.1186/s13062-015-0071-8
Experiences with workflows for automating data-intensive bioinformatics
Cited by: 51
Author(s): Ola Spjuth, Erik Bongcam‐Rudloff, Guillermo Carrasco Hernández, Lukas Forer, Mario Giovacchini, Roman Valls Guimerà, Aleksi Kallio, Eija Korpelainen, Maciej M. Kańduła, Milko Krachunov, David P. Kreil, Ognyan Kulev, Paweł P. Łabaj, Samuel Lampa, Luca Pireddu, Sebastian Schönherr, Alexey Siretskiy, Dimitar Vassilev
Software Mentions: 4
Published: over 9 years ago
10.1186/s12896-015-0207-z
A Comparison of transgenic and wild type soybean seeds: analysis of transcriptome profiles using RNA-Seq
Cited by: 22
Author(s): Kevin Lambirth, Adam M. Whaley, Ivory C. Blakley, Jessica A. Schlueter, Kenneth L. Bost, Ann E. Loraine, Kenneth J. Piller
Software Mentions: 4
Published: about 9 years ago
10.1038/sdata.2018.147
Selection analyses of paired HIV-1 gag and gp41 sequences obtained before and after antiretroviral therapy
Cited by: 2
Author(s): Philip L. Tzou, Soo-Yon Rhee, Sergei L. Kosakovsky Pond, Justen Manasa, Robert W. Shafer
Software Mentions: 4
Published: over 6 years ago
10.12688/f1000research.6831.1
Molecular Dynamics Simulations of the Temperature Induced Unfolding of Crambin Follow the Arrhenius Equation.
Cited by: 3
Author(s): Andrew R. Dalby, Mohd Shahir Shamsir
Software Mentions: 4
Published: over 9 years ago
10.1371/journal.pone.0163491
LMethyR-SVM: Predict Human Enhancers Using Low Methylated Regions based on Weighted Support Vector Machines
Cited by: 3
Author(s): Jingting Xu, Hong Hu, Yang Dai
Software Mentions: 4
Published: about 8 years ago
10.1186/s13321-017-0228-9
chemalot and chemalot_knime: Command line programs as workflow tools for drug discovery
Cited by: 12
Author(s): Man-Ling Lee, Ignacio Aliagas, Jianwen Feng, Thomas R. Gabriel, TJ O'Donnell, Benjamin D. Sellers, Bernd Wiswedel, A. Gobbi
Software Mentions: 4
Published: over 7 years ago
10.1093/gigascience/giy125
A benchmark study of k-mer counting methods for high-throughput sequencing
Cited by: 43
Author(s): Swati Manekar, S. R. Sathe
Software Mentions: 4
Published: about 6 years ago
10.1371/journal.pone.0093975
A Framework Phylogeny of the American Oak Clade Based on Sequenced RAD Data
Cited by: 190
Author(s): Andrew L. Hipp, Deren A. R. Eaton, Jeannine Cavender‐Bares, Elisabeth Fitzek, Rick Nipper, Paul S. Manos
Software Mentions: 4
Published: over 10 years ago
10.1371/journal.pntd.0007332
Genome sequencing reveals coinfection by multiple chikungunya virus genotypes in a recent outbreak in Brazil
Cited by: 19
Author(s): Laís Ceschini Machado, Mariana C. Morais-Sobral, Túlio de Lima Campos, Mylena Ribeiro Pereira, Maria de Fátima Pessoa Militão de Albuquerque, Clément Gilbert, Rafael Freitas Oliveira Franca, Gabriel Luz Wallau
Software Mentions: 4
Published: over 5 years ago
10.1186/s13742-015-0046-9
RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing
Cited by: 118
Author(s): Vikas Gupta, April D Estrada, Ivory C. Blakley, Robert W. Reid, Ketan Patel, Mason D. Meyer, Stig Uggerhøj Andersen, Allan Brown, Mary Ann Lila, Ann E. Loraine
Software Mentions: 4
Published: almost 10 years ago
10.1186/s12864-018-5101-3
Sequence homology in eukaryotes (SHOE): interactive visual tool for promoter analysis
Cited by: 2
Author(s): Natalia Polouliakh, Paul Horton, Kazuhiro Shibanai, Kodai Takata, Vanessa Ludwig, Samik Ghosh, Hiroaki Kitano
Software Mentions: 4
Published: about 6 years ago
10.1371/journal.pone.0228520
Compressive Big Data Analytics: An ensemble meta-algorithm for high-dimensional multisource datasets
Cited by: 5
Author(s): Simeone Marino, Yangyu Zhao, Nina Zhou, Yiwang Zhou, Arthur W. Toga, Lu Zhao, Yingsi Jian, Yichen Yang, Yehu Chen, Qiucheng Wu, Jessica Wild, Brandon C Cummings, Ivo D. Dinov
Software Mentions: 4
Published: about 4 years ago
10.1371/journal.pone.0186118
Finding the signal in the noise: Could social media be utilized for early hospital notification of multiple casualty events?
Cited by: 10
Author(s): Rachael A. Callcut, Sara Moore, Glenn K. Wakam, Alan Hubbard, Mitchell J. Cohen
Software Mentions: 4
Published: about 7 years ago
10.1371/journal.pcbi.1004153
Large-Scale Chemical Similarity Networks for Target Profiling of Compounds Identified in Cell-Based Chemical Screens
Cited by: 61
Author(s): Yu‐Chen Lo, Silvia Senese, Chien-Ming Li, Qi Hu, Yong Huang, Robert Damoiseaux, Jorge Z. Torres
Software Mentions: 4
Published: over 9 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
10.3389/fninf.2016.00002
Using Make for Reproducible and Parallel Neuroimaging Workflow and Quality-Assurance
Cited by: 19
Author(s): Mary K. Askren, Trevor K. M. Day, Natalie Koh, Zoé Mestre, Jennifer N. Dines, Benjamin Korman, Susan J. Melhorn, Daniel J. Peterson, Matthew Peverill, Xiaoyan Qin, Swati Rane, Melissa Reilly, M. Reiter, Kelly Sambrook, Karl A. Woelfer, Thomas J. Grabowski, Tara M. Madhyastha
Software Mentions: 4
Published: almost 9 years ago
10.1371/journal.pcbi.1008984
Gene name errors: Lessons not learned
Cited by: 14
Author(s): Mandhri Abeysooriya, Megan Soria, Mary Sravya Kasu, Mark Ziemann
Software Mentions: 4
Published: over 3 years ago
10.1371/journal.pone.0227076
All of gene expression (AOE): An integrated index for public gene expression databases
Cited by: 29
Author(s): Hidemasa Bono
Software Mentions: 4
Published: almost 5 years ago
10.3390/ijms22073674
Can miRNA Indicate Risk of Illness after Continuous Exposure to M. tuberculosis?
Cited by: 3
Author(s): Cleonardo Augusto Silva, André M. Ribeiro-dos-Santos, Wanderson Gonçalves e Gonçalves, Pablo Diego do Carmo Pinto, Rafael Pompeu Pantoja, Tatiana Vinasco-Sandoval, André M. Ribeiro-dos-Santos, Mara H. Hutz, Amanda Ferreira Vidal, Gilderlanio Santana de Araújo, Sidney Emanuel Batista dos Santos
Software Mentions: 4
Published: over 3 years ago
10.1186/1751-0473-8-20
MIA - A free and open source software for gray scale medical image analysis
Cited by: 35
Author(s): Gert Wollny, Peter Kellman, María J. Ledesma-Carbayo, Matthew M. Skinner, Jean‐Jacques Hublin, Thomas Hierl
Software Mentions: 4
Published: about 11 years ago
10.7717/peerj-cs.593
Compi: a framework for portable and reproducible pipelines
Cited by: 7
Author(s): Hugo López-Fernández, Osvaldo Graña‐Castro, Alba Nogueira-Rodríguez, Miguel Reboiro-Jato, Daniel Glez-Peña
Software Mentions: 4
Published: over 3 years ago
10.1186/s12864-018-5115-x
Genome-wide identification and differentially expression analysis of lncRNAs in tilapia
Cited by: 19
Author(s): Bi Jun Li, Dan Jiang, Zhijun Meng, Yong Zhang, Zong Xian Zhu, Haoran Lin, Jun Xia
Software Mentions: 4
Published: about 6 years ago
10.1186/s12859-020-03852-4
Natrix: a Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads
Cited by: 12
Author(s): Marius Welzel, Anja Lange, Dominik Heider, Michael Schwarz, Bernd Freisleben, Manfred Jensen, Jens Boenigk, Daniela Beißer
Software Mentions: 4
Published: about 4 years ago
10.1186/s12864-021-07845-2
ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
Cited by: 4
Author(s): Stefan Milosavljevic, Tony Kuo, Samuele Decarli, Lucas Mohn, Jun Sese, Kentaro Shimizu, Rie Shimizu‐Inatsugi, Mark D. Robinson
Software Mentions: 4
Published: over 3 years ago
10.3389/fnins.2021.546312
Clear and Consistent Imaging of Hippocampal Internal Architecture With High Resolution Multiple Image Co-registration and Averaging (HR-MICRA)
Cited by: 6
Author(s): Lawrence Ver Hoef, Hrishikesh Deshpande, Joel K. Curé, Goutham Selladurai, Julia Fleming Beattie, Richard E. Kennedy, Robert C. Knowlton, Jerzy P. Szaflarski
Software Mentions: 4
Published: almost 4 years ago
10.1128/mSphereDirect.00283-18
Ultrasensitive Capture of Human Herpes Simplex Virus Genomes Directly from Clinical Samples Reveals Extraordinarily Limited Evolution in Cell Culture
Cited by: 46
Author(s): Alexander L. Greninger, Pavitra Roychoudhury, Hong Xie, Amanda M. Casto, Anne Cent, Gregory Pepper, David M. Koelle, Meei‐Li Huang, Anna Wald, Christine Johnston, Keith R. Jerome
Software Mentions: 4
Published: over 6 years ago
10.1186/s12864-018-5228-2
DAWN: a resource for yielding insights into the diversity among wheat genomes
Cited by: 18
Author(s): Nathan S. Watson-Haigh, Radosław Suchecki, Elena Kalashyan, Melissa Garcia, Ute Baumann
Software Mentions: 3
Published: almost 6 years ago
10.1038/s41598-019-38682-9
Unexpected population fragmentation in an endangered seabird: the case of the Peruvian diving-petrel
Cited by: 17
Author(s): Robin Cristofari, Paula Plaza, Claudia E. Fernández, Emiliano Trucchi, Nicolás Gouin, Céline Le Bohec, Carlos B. Zavalaga, Joanna Alfaro‐Shigueto, Guillermo Luna‐Jorquera
Software Mentions: 3
Published: almost 6 years ago
10.1093/bioinformatics/btz030
<i>admixr</i>—R package for reproducible analyses using ADMIXTOOLS
Cited by: 99
Author(s): Martin Petr, Benjamin Vernot, Janet Kelso
Software Mentions: 3
Published: almost 6 years ago
10.1186/s12915-020-00899-w
Complete representation of a tapeworm genome reveals chromosomes capped by centromeres, necessitating a dual role in segregation and protection
Cited by: 18
Author(s): Peter D. Olson, Alan S. Tracey, Andrew Baillie, Katherine James, Stephen R. Doyle, Sarah Kay Buddenborg, Faye H. Rodgers, Nancy Holroyd, Matthew Berriman
Software Mentions: 3
Published: about 4 years ago
10.1186/1471-2105-12-98
CDAO-Store: Ontology-driven Data Integration for Phylogenetic Analysis
Cited by: 20
Author(s): Brandon Chisham, Ben Wright, Hieu Giang Le, Tran Cao Son, Enrico Pontelli
Software Mentions: 3
Published: over 13 years ago
10.1038/s41597-019-0020-y
A 204-subject multimodal neuroimaging dataset to study language processing
Cited by: 53
Author(s): Jan Mathijs Schoffelen, Robert Oostenveld, Nietzsche H. L. Lam, Julia Uddén, Annika Hultén, Peter Hagoort
Software Mentions: 3
Published: over 5 years ago
10.1186/1752-0509-1-56
Gene regulatory networks in lactation: identification of global principles using bioinformatics
Cited by: 124
Author(s): Danielle G. Lemay, Margaret C. Neville, Michael C. Rudolph, Katherine S. Pollard, J. Bruce German
Software Mentions: 3
Published: almost 17 years ago
10.1038/srep15839
Littoral lichens as a novel source of potentially bioactive Actinobacteria
Cited by: 51
Author(s): Delphine Parrot, Sanjay Antony-Babu, Laurent Intertaglia, Martín Grube, Sophie Tomasi, Marcelino T. Suzuki
Software Mentions: 3
Published: about 9 years ago
10.1371/journal.pone.0194023
ER-positive breast cancer cells are poised for RET-mediated endocrine resistance
Cited by: 18
Author(s): Sachi Horibata, Edward J. Rice, Chinatsu Mukai, Brooke A. Marks, Kelly L. Sams, Hui Zheng, Lynne J. Anguish, Scott A. Coonrod, Charles G. Danko
Software Mentions: 3
Published: over 6 years ago
10.1186/1471-2202-12-119
TRENTOOL: A Matlab open source toolbox to analyse information flow in time series data with transfer entropy
Cited by: 187
Author(s): Michael Lindner, Raúl Vicente, Viola Priesemann, Michael Wibral
Software Mentions: 3
Published: about 13 years ago
10.1093/gigascience/gix099
An architecture for genomics analysis in a clinical setting using Galaxy and Docker
Cited by: 9
Author(s): William Digan, Hector Countouris, Marc Barritault, David Baudoin, Pierre Laurent‐Puig, Hélène Blons, Anita Burgun, Bastien Rance
Software Mentions: 3
Published: about 7 years ago
10.1186/s12866-015-0370-3
New insights into the fungal community from the raw genomic sequence data of fig wasp Ceratosolen solmsi
Cited by: 5
Author(s): Lihua Niu, Xiufeng Song, Shunmin He, Peng Zhang, Ningxin Wang, Yi Li, Dawei Huang
Software Mentions: 3
Published: almost 10 years ago
10.1534/g3.120.401775
BioLitMine: Advanced Mining of Biomedical and Biological Literature About Human Genes and Genes from Major Model Organisms
Cited by: 7
Author(s): Yanhui Hu, Verena Chung, Aram Comjean, Jonathan Rodiger, Fnu Nipun, Norbert Perrimon, Stephanie E. Mohr
Software Mentions: 3
Published: almost 4 years ago
10.1534/g3.120.401287
The Effects of Quantitative Trait Architecture on Detection Power in Short-Term Artificial Selection Experiments
Cited by: 4
Author(s): Runyang Nicolas Lou, Nina Overgaard Therkildsen, Philipp W. Messer
Software Mentions: 3
Published: about 4 years ago
10.1107/S0907444909047337
<i>XDS</i>
Cited by: 12,921
Author(s): Wolfgang Kabsch
Software Mentions: 3
Published: almost 15 years ago
10.1371/journal.pone.0101754
An Integrated SNP Mining and Utilization (ISMU) Pipeline for Next Generation Sequencing Data
Cited by: 10
Author(s): Sarwar Azam, Abhishek Rathore, Trushar Shah, Mohan Telluri, BhanuPrakash Amindala, Pradeep Ruperao, Mohan A. V. S. K. Katta, Rajeev K. Varshney
Software Mentions: 3
Published: over 10 years ago
10.1093/gbe/evaa153
The Identification and Evolutionary Trends of the Solute Carrier Superfamily in Arthropods
Cited by: 9
Author(s): Shane Denecke, Olympia Driva, Hằng Ngọc Bảo Lương, Panagiotis Ioannidis, Marc Linka, Ralf Nauen, Sven Geibel, John Vontas
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-021-04316-z
Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation
Cited by: 2
Author(s): Alejandro A. Schäffer, Richard McVeigh, Barbara Robbertse, Conrad L. Schoch, Anjanette Johnston, Beverly A. Underwood, Ilene Karsch‐Mizrachi, Eric P. Nawrocki
Software Mentions: 3
Published: over 3 years ago
10.1371/journal.pgen.1005963
De Novo and Rare Variants at Multiple Loci Support the Oligogenic Origins of Atrioventricular Septal Heart Defects
Cited by: 87
Author(s): James R. Priest, Kazutoyo Osoegawa, Nebil Mohammed, Vivek Nanda, Ramendra K. Kundu, Kathleen Schultz, Edward J. Lammer, Santhosh Girirajan, Todd E. Scheetz, Daryl Waggott, François Haddad, Sushma Reddy, Daniel Bernstein, Trudy L. Burns, Jeffrey D. Steimle, Xinan Yang, Ivan P. Moskowitz, Matthew E. Hurles, Richard P. Lifton, Debbie Nickerson, Michael J. Bamshad, Evan E. Eichler, Seema Mital, Val C. Sheffield, Thomas Quertermous, Bruce D. Gelb, Michael A. Portman, Euan A. Ashley
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pcbi.1002714
Confidence-based Somatic Mutation Evaluation and Prioritization
Cited by: 30
Author(s): Martin Löwer, Bernhard Y. Renard, Jos de Graaf, Meike Wagner, Claudia Paret, Kneip Christoph, Özlem Türeci, Mustafa Diken, Cedrik M. Britten, Sebastian Kreiter, Michael Koslowski, John C. Castle, Uğur Şahin
Software Mentions: 3
Published: about 12 years ago
10.1371/journal.pone.0184119
Discovery of numerous novel small genes in the intergenic regions of the Escherichia coli O157:H7 Sakai genome
Cited by: 25
Author(s): Sarah M. Hücker, Zachary Ardern, Tatyana Goldberg, Andrea Schafferhans, Michael Bernhofer, Gisle Vestergaard, Chase W. Nelson, Michael Schloter, Burkhard Rost, Siegfried Scherer, Klaus Neuhaus
Software Mentions: 3
Published: about 7 years ago
10.3389/fpls.2017.00969
Identification and Characterization of miRNA Transcriptome in Asiatic Cotton (Gossypium arboreum) Using High Throughput Sequencing
Cited by: 14
Author(s): Muhammad Farooq, Shahid Mansoor, Hui Guo, Imran Amin, Peng W. Chee, M. Kamran Azim, Andrew H. Paterson
Software Mentions: 3
Published: over 7 years ago
10.1186/s12864-016-2516-6
CTCF-mediated chromatin loops enclose inducible gene regulatory domains
Cited by: 58
Author(s): Martin Oti, Jonas Falck, Martijn A. Huynen, Huiqing Zhou
Software Mentions: 3
Published: over 8 years ago
10.1371/journal.pcbi.1008549
Ten simple rules for quick and dirty scientific programming
Cited by: 9
Author(s): Gabriel Balaban, Ivar Grytten, Knut Dagestad Rand, Lonneke Scheffer, Geir Kjetil Sandve
Software Mentions: 3
Published: over 3 years ago