pypi: conda | Projects | Ecosyste.ms: Papers

10.12688/f1000research.20843.1

Creating and sharing reproducible research code the workflowr way
Cited by: 51
Author(s): John Blischak, Peter Carbonetto, Matthew Stephens
Software Mentions: 22
Published: about 5 years ago

10.3390/ijms22105385

Deep Learning in Pancreatic Tissue: Identification of Anatomical Structures, Pancreatic Intraepithelial Neoplasia, and Ductal Adenocarcinoma
Cited by: 15
Author(s): Mark Kriegsmann, Katharina Kriegsmann, Georg Steinbuß, Christiane Zgorzelski, Anne Kraft, Matthias M. Gaida
Software Mentions: 18
Published: over 3 years ago

10.1093/bioinformatics/bty149

NanoPack: visualizing and processing long-read sequencing data
Cited by: 1,423
Author(s): Wouter De Coster, Svenn D’Hert, Darrin T. Schultz, Marc Cruts, Christine Van Broeckhoven
Software Mentions: 18
Published: over 6 years ago

10.3390/cancers13102419

Deep Learning for the Classification of Non-Hodgkin Lymphoma on Histopathological Images
Cited by: 16
Author(s): Georg Steinbuß, Mark Kriegsmann, Christiane Zgorzelski, Alexander Brobeil, Benjamin Goeppert, Sascha Dietrich, Gunhild Mechtersheimer, Katharina Kriegsmann
Software Mentions: 18
Published: over 3 years ago

10.1099/mgen.0.000583

rMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data
Cited by: 5
Author(s): Ivan Sserwadda, Gerald Mboowa
Software Mentions: 13
Published: over 3 years ago

10.1186/s12859-021-04142-3

SPEAQeasy: a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses
Cited by: 11
Author(s): Nicholas J. Eagles, Emily E. Burke, Jacob Leonard, Brianna K. Barry, Joshua M. Stolz, Louise A Huuki, BaDoi N. Phan, Violeta Larios Serrato, Everardo Gutiérrez-Millán, Israel Aguilar-Ordóñez, Andrew E. Jaffe, Leonardo Collado‐Torres
Software Mentions: 13
Published: over 3 years ago

10.1186/s13321-020-00455-2

spyrmsd: symmetry-corrected RMSD calculations in Python
Cited by: 23
Author(s): Rocco Meli, Philip C. Biggin
Software Mentions: 13
Published: about 4 years ago

10.1186/s40679-018-0060-y

An open-source software ecosystem for the interactive exploration of ultrafast electron scattering data
Cited by: 11
Author(s): Laurent P. René de Cotret, Martin Otto, Mark J. Stern, Bradley J. Siwick
Software Mentions: 12
Published: about 6 years ago

10.1007/s00401-020-02226-7

Patient-derived organoids and orthotopic xenografts of primary and recurrent gliomas represent relevant patient avatars for precision oncology
Cited by: 69
Author(s): Anna Golebiewska, Ann-Christin Hau, Anaïs Oudin, Daniel Stieber, Yahaya A Yabo, Virginie Baus, Vanessa Barthelemy, Eliane Klein, Sébastien Bougnaud, Olivier Keunen, May Wantz, Alessandro Michelucci, Virginie Neirinckx, Arnaud Muller, Tony Kaoma, Petr V. Nazarov, Francisco Azuaje, Alfonso De Falco, Ben Flies, Lorraine Richart, Suresh Poovathingal, Thaís Arns, Kamil Grzyb, Andreas Möck, Christel Herold‐Mende, Anne Steinø, Dennis Brown, Patrick May, Hrvoje Miletić, Tathiane M. Malta, Houtan Noushmehr, Yong-Jun Kwon, Winnie Jahn, Barbara Klink, Georgette Tanner, Lucy F. Stead, Michel Mittelbronn, Alexander Skupin, Frank Hutter, Rolf Bjerkvig, Simone P. Niclou
Software Mentions: 12
Published: about 4 years ago

10.7717/peerj.11376

ProkEvo: an automated, reproducible, and scalable framework for high-throughput bacterial population genomics analyses
Cited by: 4
Author(s): Natasha Pavlovikj, João Carlos Gomes-Neto, Jitender S. Deogun, Andrew K. Benson
Software Mentions: 12
Published: over 3 years ago

10.1038/s41598-020-65015-y

Toffee – a highly efficient, lossless file format for DIA-MS
Cited by: 9
Author(s): Brett Tully
Software Mentions: 11
Published: over 4 years ago

10.1016/j.xpro.2021.100397

Protocol for comprehensive RNA sequencing analysis of murine long non-coding RNAs during aging
Cited by: 0
Author(s): Xinyue Lu, Qi Zhou, Jin Liu, Li Sun
Software Mentions: 11
Published: over 3 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: over 5 years ago

10.3389/fnins.2020.00919

HYGRIP: Full-Stack Characterization of Neurobehavioral Signals (fNIRS, EEG, EMG, Force, and Breathing) During a Bimanual Grip Force Control Task
Cited by: 10
Author(s): Pablo Ortega, Tong Zhao, A. Aldo Faisal
Software Mentions: 11
Published: about 4 years ago

10.12688/wellcomeopenres.16430.2

Polysomal mRNA Association and Gene Expression in Trypanosoma brucei
Cited by: 0
Author(s): Michele Tinti, Anna Kelner-Mirôn, Lizzie J. Marriott, Michael A. J. Ferguson
Software Mentions: 11
Published: about 3 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

10.1186/s13059-021-02368-1

treeclimbR pinpoints the data-dependent resolution of hierarchical hypotheses
Cited by: 4
Author(s): Ronald Huang, Charlotte Soneson, Pierre‐Luc Germain, Thomas Schmidt, Christian von Mering, Mark D. Robinson
Software Mentions: 10
Published: over 3 years ago

10.1186/s12862-021-01806-9

The diversity of opsins in Lake Baikal amphipods (Amphipoda: Gammaridae)
Cited by: 8
Author(s): Polina Drozdova, Alena Kizenko, Alexandra Saranchina, Anton Gurkov, Maria Firulyova, E. B. Govorukhina, Maxim A. Timofeyev
Software Mentions: 9
Published: over 3 years ago

10.1007/s13238-020-00724-8

A practical guide to amplicon and metagenomic analysis of microbiome data
Cited by: 311
Author(s): Yong‐Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo, Yang Bai
Software Mentions: 9
Published: over 4 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

10.1111/1755-0998.13030

DeviaTE: Assembly‐free analysis and visualization of mobile genetic element composition
Cited by: 26
Author(s): Lukas Weilguny, Robert Kofler
Software Mentions: 9
Published: over 5 years ago

10.3389/fninf.2017.00062

Semi-automated Anatomical Labeling and Inter-subject Warping of High-Density Intracranial Recording Electrodes in Electrocorticography
Cited by: 78
Author(s): Liberty S. Hamilton, David L. Chang, Morgan B. Lee, Edward F. Chang
Software Mentions: 9
Published: about 7 years ago

10.1186/s12859-020-03703-2

SQMtools: automated processing and visual analysis of ’omics data with R and anvi’o
Cited by: 25
Author(s): Fernando Puente-Sánchez, Natalia García-García, Javier Tamames
Software Mentions: 9
Published: about 4 years ago

10.1371/journal.pcbi.1008223

Causal network inference from gene transcriptional time-series response to glucocorticoids
Cited by: 15
Author(s): Jonathan Lu, Bianca Dumitrascu, Ian C. McDowell, Brian Jo, Alejandro Barrera, Linda K. Hong, Sarah M. Leichter, Timothy E. Reddy, Barbara E. Engelhardt
Software Mentions: 9
Published: almost 4 years ago

10.3389/fmicb.2021.649517

Decentralized Investigation of Bacterial Outbreaks Based on Hashed cgMLST
Cited by: 15
Author(s): Carlus Deneke, Laura Uelze, Holger Brendebach, Simon H. Tausch, Burkhard Malorny
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008724

Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
Cited by: 81
Author(s): Florian Huber, Lars Ridder, Stefan Verhoeven, Jurriaan H. Spaaks, F. Diblen, Simon Rogers, Justin J. J. van der Hooft
Software Mentions: 9
Published: over 3 years ago

10.1371/journal.pcbi.1008716

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
Cited by: 14
Author(s): Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam‐Rudloff, Christian Brandt
Software Mentions: 8
Published: over 3 years ago

10.3390/s20226666

Blood Stain Classification with Hyperspectral Imaging and Deep Neural Networks
Cited by: 18
Author(s): Kamil Książek, Michał Romaszewski, Przemysław Głomb, Bartosz Grabowski, Michał Cholewa
Software Mentions: 8
Published: almost 4 years ago

10.12688/f1000research.19675.1

Large-scale sequence comparisons with sourmash
Cited by: 103
Author(s): Pierce Nt, Luiz Irber, Taylor Reiter, Phillip T. Brooks, Brown Ct
Software Mentions: 8
Published: over 5 years ago

10.1186/s12864-019-5624-2

ALFA: annotation landscape for aligned reads
Cited by: 9
Author(s): Mathieu Bahin, Benoît Noël, Valentine Murigneux, Charles Bernard, Leïla Bastianelli, Hervé Le Hir, Alice Lebreton, Auguste Genovesio
Software Mentions: 8
Published: over 5 years ago

10.1007/s10278-017-0037-8

SimpleITK Image-Analysis Notebooks: a Collaborative Environment for Education and Reproducible Research
Cited by: 239
Author(s): Ziv Yaniv, Bradley Lowekamp, Hans J. Johnson, Richard Beare
Software Mentions: 8
Published: almost 7 years ago

10.1107/S1600576718017296

refnx: neutron and X-ray reflectometry analysis in Python
Cited by: 95
Author(s): Andrew Nelson, Stuart W. Prescott
Software Mentions: 8
Published: almost 6 years ago

10.1107/S2059798320003769

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries
Cited by: 0
Author(s): J.M. de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquı́n Otón, Erik Lindahl
Software Mentions: 7
Published: over 4 years ago

10.1186/s40168-020-00993-9

PathoFact: a pipeline for the prediction of virulence factors and antimicrobial resistance genes in metagenomic data
Cited by: 61
Author(s): Laura de Nies, Sara Lopes, Susheel Bhanu Busi, Valentina Galata, Anna Heintz‐Buschart, Cédric Christian Laczny, Patrick May, Paul Wilmes
Software Mentions: 7
Published: over 3 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

10.1371/journal.pcbi.1008645

Ten simple rules for getting started with command-line bioinformatics
Cited by: 7
Author(s): Parice A. Brandies, Carolyn J. Hogg
Software Mentions: 7
Published: over 3 years ago

10.1371/journal.pone.0253411

PDBrenum: A webserver and program providing Protein Data Bank files renumbered according to their UniProt sequences
Cited by: 12
Author(s): Bulat Faezov, Roland L. Dunbrack
Software Mentions: 7
Published: over 3 years ago

10.12688/f1000research.14880.4

SeqAcademy: an educational pipeline for RNA-Seq and ChIP-Seq analysis
Cited by: 0
Author(s): Syed Hussain Ather, Olaitan I. Awe, Thomas J. Butler, Tamiru Denka, Stephen A. Semick, Wanhu Tang, Ben Busby
Software Mentions: 7
Published: about 4 years ago

10.12688/f1000research.15830.2

An accessible, interactive GenePattern Notebook for analysis and exploration of single-cell transcriptomic data
Cited by: 2
Author(s): Clarence K. Mah, Alexander T. Wenzel, Edwin F. Juarez, Thorin Tabor, Michael Reich, Jill P. Mesirov
Software Mentions: 7
Published: over 5 years ago

10.1093/gigascience/giaa135

Dadasnake, a Snakemake implementation of DADA2 to process amplicon sequencing data for microbial ecology
Cited by: 33
Author(s): Christina Weißbecker, Beatrix Schnabel, Anna Heintz‐Buschart
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13321-019-0351-x

TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data
Cited by: 25
Author(s): Dominique Sydow, Andrea Morger, Maximilian Driller, Andrea Volkamer
Software Mentions: 7
Published: over 5 years ago

10.1186/s13059-019-1738-8

Essential guidelines for computational method benchmarking
Cited by: 107
Author(s): Lukas Weber, Wouter Saelens, Robrecht Cannoodt, Charlotte Soneson, Alexander Hapfelmeier, Paul Geeleher, Anne‐Laure Boulesteix, Yvan Saeys, Mark D. Robinson
Software Mentions: 6
Published: over 5 years ago

10.1038/s41598-020-70259-9

liputils: a Python module to manage individual fatty acid moieties from complex lipids
Cited by: 3
Author(s): Stefano Manzini, M. Busnelli, A Colombo, Mostafa Kiamehr, Giulia Chiesa
Software Mentions: 6
Published: about 4 years ago

10.1093/gigascience/giaa152

Tool recommender system in Galaxy using deep learning
Cited by: 7
Author(s): Anup Kumar, Helena Rasche, Björn Grüning, Rolf Backofen
Software Mentions: 6
Published: almost 4 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

10.1523/ENEURO.0085-20.2020

neurotic: Neuroscience Tool for Interactive Characterization
Cited by: 4
Author(s): Jeffrey P. Gill, Samuel Garcia, Lena H. Ting, Mengnan Wu, Hillel J. Chiel
Software Mentions: 6
Published: over 4 years ago

10.1093/gigascience/giaa064

Integrative computational epigenomics to build data-driven gene regulation hypotheses
Cited by: 10
Author(s): Tyrone Chen, Sonika Tyagi
Software Mentions: 6
Published: over 4 years ago

10.3389/fgene.2018.00671

UTRme: A Scoring-Based Tool to Annotate Untranslated Regions in Trypanosomatid Genomes
Cited by: 20
Author(s): Santiago Radío, Rafael Sebastián Fort, Beatríz Garat, José Sotelo‐Silveira, Pablo Smircich
Software Mentions: 5
Published: almost 6 years ago

10.1099/mgen.0.000500

Identifying novel β-lactamase substrate activity through in silico prediction of antimicrobial resistance
Cited by: 7
Author(s): Kara K. Tsang, Finlay Maguire, Haley L. Zubyk, Sommer Chou, Arman Edalatmand, Gerard D. Wright, Robert G. Beiko, Andrew G. McArthur
Software Mentions: 5
Published: almost 4 years ago

10.3390/proteomes8030015

Precursor Intensity-Based Label-Free Quantification Software Tools for Proteomic and Multi-Omic Analysis within the Galaxy Platform
Cited by: 9
Author(s): Subina Mehta, Caleb Easterly, Ray Sajulga, Robert Millikin, Andrea Argentini, Ignacio Eguinoa, Lennart Martens, Michael R. Shortreed, Lloyd M. Smith, Thomas McGowan, Praveen Kumar, James E. Johnson, Timothy J. Griffin, Pratik Jagtap
Software Mentions: 5
Published: over 4 years ago

10.1093/bib/bbab055

RNA2HLA: HLA-based quality control of RNA-seq datasets
Cited by: 9
Author(s): Irina Chelysheva, Andrew J. Pollard, Daniel O’Connor
Software Mentions: 5
Published: over 3 years ago

10.7554/eLife.64618

Genomic epidemiology of COVID-19 in care homes in the east of England
Cited by: 17
Author(s): William L. Hamilton, Gerry Tonkin‐Hill, Darren Smith, Dinesh Aggarwal, Charlotte J. Houldcroft, Ben Warne, Luke W. Meredith, Myra Hosmillo, Aminu S. Jahun, Martin D. Curran, Surendra Parmar, Laura Caller, Sarah Caddy, Fahad Khokhar, Anna Yakovleva, Grant Hall, Theresa Feltwell, Malte L. Pinckert, Iliana Georgana, Yasmin Chaudhry, Colin Brown, Sónia Gonçalves, Roberto Amato, Ewan M. Harrison, Nicholas Brown, Mathew A. Beale, Michael Spencer Chapman, David Jackson, Ian Johnston, Alex Alderton, John Sillitoe, Cordelia Langford, Gordon Dougan, Sharon J. Peacock, Dominic P Kwiatowski, Ian Goodfellow, M. Estée Török
Software Mentions: 5
Published: over 3 years ago

10.7717/peerj.3720

Atropos: specific, sensitive, and speedy trimming of sequencing reads
Cited by: 168
Author(s): John P. Didion, Marcel Martin, Francis S. Collins
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pcbi.1006384

Context-explorer: Analysis of spatially organized protein expression in high-throughput screens
Cited by: 9
Author(s): Joel Östblom, Emanuel Joseph Paul Nazareth, Mukul Tewary
Software Mentions: 5
Published: almost 6 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

10.1186/s13059-019-1905-y

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Cited by: 442
Author(s): Shujun Ou, Weija Su, Yi Liao, Kapeel Chougule, Jireh Agda, Adam J. Hellinga, Carlos Santiago Blanco Lugo, Tyler A. Elliott, Doreen Ware, Thomas Peterson, Ning Jiang, Candice N. Hirsch, Matthew B. Hufford
Software Mentions: 5
Published: almost 5 years ago

10.1371/journal.pcbi.1007980

AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments
Cited by: 15
Author(s): Andrew J. Page, Sarah Bastkowski, Muhammad Yasir, A. Keith Turner, Thanh Le Viet, George M. Savva, Mark A. Webber, Ian G. Charles
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1008926

Sequence deeper without sequencing more: Bayesian resolution of ambiguously mapped reads
Cited by: 6
Author(s): Ramila Shah, Alexander J. Ruthenburg
Software Mentions: 4
Published: over 3 years ago

10.1186/s12859-018-2134-1

SECIMTools: a suite of metabolomics data analysis tools
Cited by: 33
Author(s): Alexander Kirpich, Miguel Ibarra, Oleksandr Moskalenko, Justin M. Fear, Joseph E. Gerken, Xinlei Mi, Ali Ashrafi, Alison M. Morse, Lauren McIntyre
Software Mentions: 4
Published: over 6 years ago

10.1371/journal.pcbi.1004728

Ensembler: Enabling High-Throughput Molecular Simulations at the Superfamily Scale
Cited by: 20
Author(s): Daniel L. Parton, Patrick Grinaway, Sonya M. Hanson, Kyle A. Beauchamp, John D. Chodera
Software Mentions: 4
Published: over 8 years ago

10.12688/f1000research.20873.2

The why, when, and how of computing in biology classrooms
Cited by: 12
Author(s): April M. Wright, Rachel S. Schwartz, Jamie R. Oaks, Catherine E. Newman, Sarah P. Flanagan
Software Mentions: 4
Published: over 4 years ago

10.1093/molbev/msaa222

Log Transformation Improves Dating of Phylogenies
Cited by: 4
Author(s): Uyen Mai, Siavash Mirarab
Software Mentions: 4
Published: about 4 years ago

10.3389/fonc.2020.599907

18F-FDG PET/CT Metrics Are Correlated to the Pathological Response in Esophageal Cancer Patients Treated With Induction Chemotherapy Followed by Neoadjuvant Chemo-Radiotherapy
Cited by: 15
Author(s): N. Simoni, Gabriella Rossi, Giulio Benetti, Michele Zuffante, R. Micera, M. Pavarana, Stefania Guariglia, Emanuele Zivelonghi, Valentina Mengardo, Jacopo Weindelmayer, Simone Giacopuzzi, Giovanni De Manzoni, Carlo Cavedon, Renzo Mazzarotto
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0242143

Freshwater diatom biomonitoring through benthic kick-net metabarcoding
Cited by: 11
Author(s): Victoria Carley Maitland, Chloe Victoria Robinson, Teresita M. Porter, Mehrdad Hajibabaei
Software Mentions: 4
Published: almost 4 years ago

10.1093/bib/bbaa232

Computational strategies to combat COVID-19: useful tools to accelerate SARS-CoV-2 and coronavirus research
Cited by: 99
Author(s): Franziska Hufsky, Kevin Lamkiewicz, Alexandre Almeida, Abdel Aouacheria, Cecilia N. Arighi, Alex Bateman, Jan Baumbach, Niko Beerenwinkel, Christian Brandt, Marco Cacciabue, Sara Chuguransky, Oliver Drechsel, Alex Bateman, Adrian Fritz, Stephan Fuchs, Georges Hattab, Anne-Christin Hauschild, Dominik Heider, Marie Hoffmann, Martin Hölzer, Stefan Hoops, Lars Kaderali, Ioanna Kalvari, Max von Kleist, Renó Kmiecinski, Denise Kühnert, Gorka Lasso, Pieter Libin, Markus List, Hannah F Löchel, Marı́a Jesús Martı́n, Roman Martin, Julian Matschinske, Alice C. McHardy, Pedro Mendes, Jaina Mistry, Vincent Navratil, Eric P. Nawrocki, Áine O’Toole, Nancy Ontiveros-Palacios, Anton I. Petrov, Guillermo Rangel-Piñeros, Nicole Redaschi, Susanne Reimering, Knut Reinert, Alejandro Reyes, Lorna Richardson, David L. Robertson, Sepideh Sadegh, Joshua B. Singer, Kristof Theys, Chris Upton, Marius Welzel, Lowri Williams, Manja Marz
Software Mentions: 4
Published: about 4 years ago

10.1007/s11547-021-01370-8

CT radiomic models to distinguish COVID-19 pneumonia from other interstitial pneumonias
Cited by: 18
Author(s): Nicolò Cardobi, Giulio Benetti, Giuseppe Cardano, Cinzia Arena, Claudio Micheletto, Carlo Cavedon, Stefania Montemezzi
Software Mentions: 4
Published: over 3 years ago

10.12688/f1000research.20233.1

A Sequence Distance Graph framework for genome assembly and analysis
Cited by: 3
Author(s): Luis Yanes, Gonzalo Garcia Accinelli, Jonathan Wright, Ben J. Ward, Bernardo Clavijo
Software Mentions: 4
Published: about 5 years ago

10.12688/f1000research.10783.2

A very simple, re-executable neuroimaging publication
Cited by: 10
Author(s): Samik Ghosh, Jean‐Baptiste Poline, David B. Keator, Yaroslav O. Halchenko, Adrian L. R. Thomas, Daniel Kessler, David N. Kennedy
Software Mentions: 4
Published: over 7 years ago

10.12688/f1000research.24751.2

Reproducibly sampling SARS-CoV-2 genomes across time, geography, and viral diversity
Cited by: 9
Author(s): Evan Bolyen, Matthew R. Dillon, Nicholas A. Bokulich, Jason T. Ladner, Brendan B. Larsen, Crystal M. Hepp, Darrin Lemmer, Jason W. Sahl, Andrew Sanchez, Chris Holdgraf, Chris Sewell, Aakash G. Choudhury, John Stachurski, Matthew R. McKay, Anthony Simard, David M. Engelthaler, Michael Worobey, Paul Keim, J. Gregory Caporaso
Software Mentions: 4
Published: about 4 years ago

10.3389/fmicb.2020.584699

PUMAA: A Platform for Accessible Microbiome Analysis in the Undergraduate Classroom
Cited by: 8
Author(s): Keith Mitchell, Jiem R. Ronas, Christopher Dao, Amanda C. Freise, Serghei Mangul, Casey Shapiro, Jordan Moberg Parker
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-020-03585-4

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data
Cited by: 74
Author(s): Silas Kieser, Joseph Brown, Evgeny M. Zdobnov, Mirko Trajkovski, Lee Ann McCue
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pone.0232644

TargetDB: A target information aggregation tool and tractability predictor
Cited by: 9
Author(s): Stéphane De Cesco, John B. Davis, P.E. Brennan
Software Mentions: 3
Published: about 4 years ago

10.1111/tpj.14747

Rapid identification of an Arabidopsis NLR gene as a candidate conferring susceptibility to Sclerotinia sclerotiorum using time‐resolved automated phenotyping
Cited by: 26
Author(s): Adelin Barbacci, Olivier Navaud, Malick Mbengue, Marielle Barascud, Laurence Godiard, Mehdi Khafif, Aline Lacaze, Sylvain Raffaele
Software Mentions: 3
Published: over 4 years ago

10.3390/ijerph18052713

A Real-Time Artificial Intelligence-Assisted System to Predict Weaning from Ventilator Immediately after Lung Resection Surgery
Cited by: 18
Author(s): Ying-Jen Chang, Kuo‐Chuan Hung, Li‐Kai Wang, Chia-Hung Yu, Chao-Kun Chen, Hung-Tze Tay, Jhi-Joung Wang, Chia‐Jung Chen
Software Mentions: 3
Published: over 3 years ago

10.1016/j.patter.2020.100103

Tackling the Challenges of 21st-Century Open Science and Beyond: A Data Science Lab Approach
Cited by: 8
Author(s): Michael Hollaway, Graham Dean, Gordon S. Blair, Mark Brown, Peter A. Henrys, John Watkins
Software Mentions: 3
Published: about 4 years ago

10.1186/s40168-021-01065-2

Parabacteroides produces acetate to alleviate heparanase-exacerbated acute pancreatitis through reducing neutrophil infiltration
Cited by: 73
Author(s): Yuanyuan Lei, Li Tang, Shuang Liu, Shiping Hu, Ling-Yi Wu, Yaojiang Liu, Min Ye, Shengjie Huang, Xuefeng Tang, Tao Tang, Xiao‐Fan Zhao, Israël Vlodavsky, Shuo Zeng, Bo Tang, Shiming Yang
Software Mentions: 3
Published: over 3 years ago

10.1186/s13073-021-00953-4

GenTB: A user-friendly genome-based predictor for tuberculosis resistance powered by machine learning
Cited by: 19
Author(s): Matthias I. Gröschel, Martin Owens, Luca Freschi, Roger Vargas, Maximilian G. Marin, Jody Phelan, Zamin Iqbal, Avika Dixit, Maha Farhat
Software Mentions: 3
Published: about 3 years ago

10.1016/j.xpro.2021.100505

Computational generation of proteins with predetermined three-dimensional shapes using ProteinSolver
Cited by: 6
Author(s): Alexey Strokach, David Becerra, Carles Corbi‐Verge, Albert Perez-Riba, Philip M. Kim
Software Mentions: 3
Published: over 3 years ago

10.1038/s41598-021-90170-1

Unique evolutionary trajectories of breast cancers with distinct genomic and spatial heterogeneity
Cited by: 0
Author(s): Tanya N. Phung, Timothy H. Webster, Elizabeth Lenkiewicz, Smriti Malasi, Mariacarla Andreozzi, Ann E. McCullough, Karen S. Anderson, Barbara A. Pockaj, Melissa A. Wilson, Michael T. Barrett
Software Mentions: 3
Published: over 3 years ago

10.1128/mSystems.00190-20

Bactopia: a Flexible Pipeline for Complete Analysis of Bacterial Genomes
Cited by: 64
Author(s): Robert A. Petit, Timothy D. Read
Software Mentions: 3
Published: about 4 years ago

10.1186/s12864-021-07685-0

Insights into the genome architecture and evolution of Shiga toxin encoding bacteriophages of Escherichia coli
Cited by: 11
Author(s): Graça Pinto, Marta Sampaio, Óscar Dias, Carina Almeida, Joana Azeredo, Hugo Oliveira
Software Mentions: 2
Published: over 3 years ago

10.3389/fphys.2021.710968

Regulation of the Muscarinic M3 Receptor by Myocardin-Related Transcription Factors
Cited by: 4
Author(s): Li Liu, Catarina Rippe, Ola Hansson, Dmytro Kryvokhyzha, Steven A. Fisher, Mari Ekman, Karl Swärd
Software Mentions: 2
Published: about 3 years ago

10.1371/journal.pone.0230557

bertha: Project skeleton for scientific software
Cited by: 9
Author(s): Michael Riesch, Thi Thanh Ngan Nguyen, Christian Jirauschek
Software Mentions: 2
Published: over 4 years ago

10.3390/jcm10061186

A Validation Employing Convolutional Neural Network for the Radiographic Detection of Absence or Presence of Teeth
Cited by: 1
Author(s): María Prados-Privado, Javier García Villalón, Antonio Blázquez Torres, Carlos Hugo Martínez-Martínez, Carlos Ivorra
Software Mentions: 2
Published: over 3 years ago

10.1186/s13321-020-00456-1

An open source chemical structure curation pipeline using RDKit
Cited by: 132
Author(s): A. Patrícia Bento, Anne Hersey, Eloy Félix, Gregory A. Landrum, Anna Gaulton, Francis Atkinson, Louisa J. Bellis, Marleen De Veij, Andrew R. Leach
Software Mentions: 2
Published: about 4 years ago

10.1186/s13321-020-0416-x

Visualization of very large high-dimensional data sets as minimum spanning trees
Cited by: 132
Author(s): Daniel Probst, Jean‐Louis Reymond
Software Mentions: 2
Published: over 4 years ago

10.3390/ma14185278

Artificial Intelligence Aided Design of Tissue Engineering Scaffolds Employing Virtual Tomography and 3D Convolutional Neural Networks
Cited by: 16
Author(s): María Dolores Bermejillo Barrera, Francisco Franco-Martínez, Andrés Díaz Lantada
Software Mentions: 1
Published: about 3 years ago

10.7717/peerj.5175

SECAPR—a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments
Cited by: 47
Author(s): Tobias Andermann, Ángela Cano, Alexander Zizka, Christine D. Bacon, Alexandre Antonelli
Software Mentions: 1
Published: over 6 years ago

10.1186/s12859-021-04271-9

PDBeCIF: an open-source mmCIF/CIF parsing and processing package
Cited by: 1
Author(s): Glen van Ginkel, Lukáš Pravda, Jose M. Dana, Mihály Váradi, Peter M. Keller, Stephen Anyango, Sameer Velankar
Software Mentions: 1
Published: over 3 years ago

10.3390/molecules26010144

SYN-View: A Phylogeny-Based Synteny Exploration Tool for the Identification of Gene Clusters Linked to Antibiotic Resistance
Cited by: 6
Author(s): Jason Stahlecker, Erik Mingyar, Nadine Ziemert, Mehmet Direnç Mungan
Software Mentions: 1
Published: almost 4 years ago

10.3389/fmicb.2021.578859

Resequencing of Microbial Isolates: A Lab Module to Introduce Novices to Command-Line Bioinformatics
Cited by: 0
Author(s): Katherine L. Petrie, Ruiqin Xie
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1006830

ReaDDy 2: Fast and flexible software framework for interacting-particle reaction dynamics
Cited by: 55
Author(s): Moritz Hoffmann, Christoph Fröhner, Frank Noé
Software Mentions: 1
Published: over 5 years ago

Projects: pypi: conda

Papers Mentioning conda 92