pypi: linux | Projects | Ecosyste.ms: Papers

10.1371/journal.pone.0251194

A computational reproducibility study of PLOS ONE articles featuring longitudinal data analyses
Cited by: 15
Author(s): Heidi Seibold, Severin Czerny, Siona Decke, Roman Dieterle, Thomas Eder, Steffen Fohr, Nico Hahn, Rabea Hartmann, Christoph Heindl, Philipp Kopper, Dario Lepke, Verena Loidl, Maximilian Mandl, Sarah Musiol, Jessica Peter, Alexander Piehler, Elio Rojas, Stefanie Schmid, Hannah Schmidt, Melissa Schmoll, Lennart Schneider, Xiao-Yin To, Viêt Anh Tran, Antje Völker, Moritz Wagner, Joshua Wagner, Maria Waize, Hannah Wecker, Rui Yang, Simone Zellner, Malte Nalenz
Software Mentions: 46
Published: over 3 years ago

10.1038/s41597-019-0171-x

A multi-omics digital research object for the genetics of sleep regulation
Cited by: 8
Author(s): Jan M, Nastassia Gobet, Shanaz Diessler, Paul Franken, Ioannis Xénarios
Software Mentions: 17
Published: about 5 years ago

10.1186/s13007-018-0376-6

PhenoFly Planning Tool: flight planning for high-resolution optical remote sensing with unmanned areal systems
Cited by: 43
Author(s): Lukas Roth, Andreas Hund, Helge Aasen
Software Mentions: 15
Published: about 6 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

10.3389/fgene.2020.489357

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results
Cited by: 13
Author(s): Alejandro Abdala Asbun, Marc Besseling, Sergio Balzano, Judith van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
Software Mentions: 11
Published: about 4 years ago

10.1186/1471-2105-7-509

CoXpress: differential co-expression in gene expression data
Cited by: 149
Author(s): Michael Watson
Software Mentions: 11
Published: about 18 years ago

10.1186/s12859-018-2296-x

Reproducible bioinformatics project: a community for reproducible bioinformatics analysis pipelines
Cited by: 47
Author(s): Neha Kulkarni, Luca Alessandrì, Riccardo Panero, Maddalena Arigoni, Martina Olivero, Giulio Ferrero, Francesca Cordero, Marco Beccuti, Raffaele Calogero
Software Mentions: 10
Published: about 6 years ago

10.1371/journal.pone.0253010

Community evolution on Stack Overflow
Cited by: 11
Author(s): Iraklis Moutidis, Hywel T. P. Williams
Software Mentions: 10
Published: over 3 years ago

10.1016/j.ajhg.2020.03.012

Mantis-ml: Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning
Cited by: 24
Author(s): Dimitrios Vitsios, Steve Petrovski
Software Mentions: 10
Published: over 4 years ago

10.1371/journal.pgen.1008831

Behavioral and brain- transcriptomic synchronization between the two opponents of a fighting pair of the fish Betta splendens
Cited by: 18
Author(s): Trieu-Duc Vu, Yoshiaki Iwasaki, Shuji Shigenobu, Akiko Maruko, Koichiro Oshima, Erica Iioka, Chao Li Huang, Takashi Abe, Satoshi Tamaki, Yi-Sheng Lin, Chih Kuan Chen, Mei-Yeh Jade Lu, Masaru Hojo, Hao Ven Wang, Shun Fen Tzeng, Hao Huang, Akio Kanai, Takashi Gojobori, Tzen‐Yuh Chiang, Han Sun, Wen-Hsiung Li, Norihiro Okada
Software Mentions: 10
Published: over 4 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/s13029-016-0059-5

A bedr way of genomic interval processing
Cited by: 19
Author(s): Syed Haider, Daryl Waggott, Emilie Lalonde, Clement Fung, Fei‐Fei Liu, Paul C. Boutros
Software Mentions: 9
Published: about 8 years ago

10.3390/ijms22116160

Spatially Enriched Paralog Rearrangements Argue Functionally Diverse Ribosomes Arise during Cold Acclimation in Arabidopsis
Cited by: 10
Author(s): Federico Martinez‐Seidel, Olga Beine-Golovchuk, Yin-Chen Hsieh, Kheloud El Eshraky, Michał Górka, Bo-Eng Cheong, Erika Vanessa Jiménez-Posada, Dirk Walther, Aleksandra Skirycz, Ute Roessner, Joachim Kopka, Alexandre Augusto Pereira Firmino
Software Mentions: 9
Published: over 3 years ago

10.1186/s13059-018-1596-9

Comparison of computational methods for the identification of topologically associating domains
Cited by: 155
Author(s): Marie Zufferey, Daniele Tavernari, Elisa Oricchio, Giovanni Ciriello
Software Mentions: 9
Published: about 6 years ago

10.1186/1472-6807-9-27

PTools: an opensource molecular docking library
Cited by: 34
Author(s): Adrien Saladin, Sébastien Fiorucci, Pierre Poulain, Chantal Prévost, Martin Zacharias
Software Mentions: 9
Published: over 15 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

10.7717/peerj.8965

CFSP: a collaborative frequent sequence pattern discovery algorithm for nucleic acid sequence classification
Cited by: 2
Author(s): Huan Peng
Software Mentions: 9
Published: over 4 years ago

10.3389/fninf.2017.00046

Software for Brain Network Simulations: A Comparative Study
Cited by: 42
Author(s): Ruben A. Tikidji-Hamburyan, Vikram K. Narayana, Zeki Bozkuş, Tarek El‐Ghazawi
Software Mentions: 9
Published: over 7 years ago

10.7554/eLife.68312

A plant-like mechanism coupling m6A reading to polyadenylation safeguards transcriptome integrity and developmental gene partitioning in Toxoplasma
Cited by: 12
Author(s): Dayana C Farhat, Matthew W. Bowler, Guillaume Communie, Dominique Pontier, Lucid Belmudes, Caroline Mas, Charlotte Corrao, Yohann Couté, Alexandre Bougdour, Thierry Lagrange, Mohamed‐Ali Hakimi, Christopher Swale
Software Mentions: 8
Published: over 3 years ago

10.1111/2041-210X.12490

hext , a software supporting tree‐based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test
Cited by: 4
Author(s): Kevin Schneider, Stephan Koblmüller, Kristina M. Sefc
Software Mentions: 8
Published: about 9 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

10.1371/journal.pcbi.1003706

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue
Cited by: 54
Author(s): Fredrik Karlsson, Intawat Nookaew, Jens Nielsen
Software Mentions: 7
Published: over 10 years ago

10.1371/journal.pone.0243672

Characterisation and chemometric evaluation of 17 elements in ten seaweed species from Greenland
Cited by: 11
Author(s): Katharina Kreissig, Lisbeth Truelstrup Hansen, Pernille Erland Jensen, Susse Wegeberg, Ole Geertz‐Hansen, Jens Jørgen Sloth
Software Mentions: 7
Published: almost 4 years ago

10.1186/s13007-019-0440-x

Comparing time series transcriptome data between plants using a network module finding algorithm
Cited by: 6
Author(s): Jiyoung Lee, Lenwood S. Heath, Ruth Grene, Song Li
Software Mentions: 7
Published: over 5 years ago

10.1186/s13293-020-00312-9

Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data
Cited by: 27
Author(s): Kimberly C. Olney, Sarah M. Brotman, Jocelyn P. Andrews, Valeria A. Valverde-Vesling, Melissa A. Wilson
Software Mentions: 7
Published: over 4 years ago

10.7717/peerj.642

Characterization of the transcriptome, nucleotide sequence polymorphism, and natural selection in the desert adapted mouse<i>Peromyscus eremicus</i>
Cited by: 34
Author(s): Matthew D. MacManes, Michael B. Eisen
Software Mentions: 7
Published: about 10 years ago

10.1038/s41598-018-38195-x

Shared cis-regulatory architecture identified across defense response genes is associated with broad-spectrum quantitative resistance in rice
Cited by: 5
Author(s): Bradley W. Tonnessen, A. M. Bossa-Castro, Ramil Mauleon, Nickolai Alexandrov, Jan E. Leach
Software Mentions: 7
Published: almost 6 years ago

10.1093/jxb/erw176

Image Harvest: an open-source platform for high-throughput plant image processing and analysis
Cited by: 68
Author(s): Avi C. Knecht, Malachy T. Campbell, Adam Caprez, David Swanson, Harkamal Walia
Software Mentions: 7
Published: over 8 years ago

10.1186/s12859-020-3434-9

SEQing: web-based visualization of iCLIP and RNA-seq data in an interactive python framework
Cited by: 7
Author(s): Martin Lewinski, Yannik Bramkamp, Tino Köster, Dorothee Staiger
Software Mentions: 6
Published: almost 5 years ago

10.1038/srep26136

SOX7 co-regulates Wnt/β-catenin signaling with Axin-2: both expressed at low levels in breast cancer
Cited by: 25
Author(s): Huidi Liu, Emilio Mastriani, Zi-Qiao Yan, Shuai Yin, Zheng Zeng, Hong Wang, Qinghai Li, Hongyu Liu, Xiaoyu Wang, Hongchu Bao, Yujie Zhou, Junjie Kou, Dongsheng Li, Ting Li, Jianrui Liu, Yongfang Liu, Lin Yin, Li Qiu, Liling Gong, Shulin Liu
Software Mentions: 6
Published: over 8 years ago

10.1186/s13059-017-1284-1

SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes
Cited by: 75
Author(s): N. Davidson, Anthony D. K. Hawkins, Alicia Oshlack
Software Mentions: 6
Published: over 7 years ago

10.3390/genes11040428

LSTrAP-Cloud: A User-Friendly Cloud Computing Pipeline to Infer Coexpression Networks
Cited by: 9
Author(s): Qiao Wen Tan, Wooi-Boon Goh, Marek Mutwil
Software Mentions: 6
Published: over 4 years ago

10.1038/sdata.2016.8

Transcriptome regulation and chromatin occupancy by E2F3 and MYC in mice
Cited by: 8
Author(s): Xing Tang, Huayang Liu, Arunima Srivastava, Thierry Pécot, Zhong Chen, Qianben Wang, Kun Huang, Maria Teresa Sáenz-Robles, Paul G. Cantalupo, James M. Pipas, Gustavo Leone
Software Mentions: 6
Published: almost 9 years ago

10.1093/molbev/msy147

Species Tree Inference with BPP Using Genomic Sequences and the Multispecies Coalescent
Cited by: 246
Author(s): Tomáš Flouri, Xiyun Jiao, Bruce Rannala, Ziheng Yang
Software Mentions: 6
Published: over 6 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: almost 14 years ago

10.3390/s21020488

CMOS Image Sensors in Surveillance System Applications
Cited by: 16
Author(s): Susrutha Babu Sukhavasi, Khaled Elleithy, Abdelshakour Abuzneid, Abdelrahman Elleithy
Software Mentions: 6
Published: almost 4 years ago

10.1371/journal.pone.0029685

A Powerful Method for Transcriptional Profiling of Specific Cell Types in Eukaryotes: Laser-Assisted Microdissection and RNA Sequencing
Cited by: 104
Author(s): Marc W. Schmid, Anja Schmidt, Ulrich C. Klostermeier, Matthias Barann, Philip Rosenstiel, Ueli Grossniklaus
Software Mentions: 6
Published: almost 13 years ago

10.1371/journal.pone.0254556

Simple mapping-based quantification of a mock microbial community using total RNA-seq data
Cited by: 4
Author(s): Shigeharu Moriya
Software Mentions: 5
Published: over 3 years ago

10.1038/s41598-021-88939-5

GPCR_LigandClassify.py; a rigorous machine learning classifier for GPCR targeting compounds
Cited by: 6
Author(s): Marawan Ahmed, Horia Jalily Hasani, Subha Kalyaanamoorthy, Khaled Barakat
Software Mentions: 5
Published: over 3 years ago

10.1111/eva.12659

Recent advances in conservation and population genomics data analysis
Cited by: 77
Author(s): Sarah A. Hendricks, Eric C. Anderson, Tiago Antão, Louis Bernatchez, Brenna R. Forester, Brittany A. Garner, Brian K. Hand, Paul A. Hohenlohe, Marty Kardos, Ben F. Koop, Arun Sethuraman, Robin S. Waples, Gordon Luikart
Software Mentions: 5
Published: over 6 years ago

10.1371/journal.pone.0204920

Predicting acute kidney injury at hospital re-entry using high-dimensional electronic health record data
Cited by: 8
Author(s): Samuel J. Weisenthal, Caroline M. Quill, Samir A. Farooq, Henry Kautz, Martin S. Zand
Software Mentions: 5
Published: about 6 years ago

10.1186/1471-2105-8-179

Genome Expression Pathway Analysis Tool – Analysis and visualization of microarray gene expression data under genomic, proteomic and metabolic context
Cited by: 23
Author(s): Markus Weniger, Julia C. Engelmann, Jörg Schultz
Software Mentions: 5
Published: over 17 years ago

10.1038/s41598-021-93003-3

A pan-cancer transcriptomic study showing tumor specific alterations in central metabolism
Cited by: 10
Author(s): Ilir Sheraj, Tülïn Güray, Sreeparna Banerjee
Software Mentions: 5
Published: over 3 years ago

10.1186/1471-2105-9-526

SNPFile – A software library and file format for large scale association mapping and population genetics studies
Cited by: 5
Author(s): Jesper Buus Nielsen, Thomas Mailund
Software Mentions: 5
Published: about 16 years ago

10.1186/1471-2105-6-98

ProGenExpress: Visualization of quantitative data on prokaryotic genomes
Cited by: 6
Author(s): Michael Watson
Software Mentions: 5
Published: over 19 years ago

10.1038/s41598-021-95748-3

Comparison of machine and deep learning for the classification of cervical cancer based on cervicography images
Cited by: 31
Author(s): Ye Rang Park, Young Jae Kim, Woong Ju, Kae Hyun Nam, Soonyung Kim, Kwang Gi Kim
Software Mentions: 5
Published: over 3 years ago

10.1186/s13321-016-0115-9

MetFrag relaunched: incorporating strategies beyond in silico fragmentation
Cited by: 597
Author(s): Christoph Ruttkies, Emma L. Schymanski, Sebastian I. Wolf, Juliane Hollender, Steffen Neumann
Software Mentions: 5
Published: almost 9 years ago

10.1186/1939-8433-6-15

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress
Cited by: 82
Author(s): Palitha Dharmawardhana, Liya Ren, Vindhya Amarasinghe, Marcela K. Monaco, Jim Thomason, Dean Ravenscroft, Susan R. McCouch, Doreen Ware, Pankaj Jaiswal
Software Mentions: 5
Published: over 11 years ago

10.1093/bib/bbaa150

Recent advances in user-friendly computational tools to engineer protein function
Cited by: 30
Author(s): Carlos Sequeiros-Borja, Bartłomiej Surpeta, Jan Brezovský
Software Mentions: 5
Published: over 4 years ago

10.1186/s12864-021-08015-0

Identification of ABC transporter G subfamily in white lupin and functional characterization of L.albABGC29 in phosphorus use
Cited by: 11
Author(s): Mehtab Muhammad Aslam, Muhammad Waseem, Qian Zhang, Ke Wang, Jianhua Zhang, Weifeng Xu
Software Mentions: 5
Published: about 3 years ago

10.1186/gb-2007-8-9-r190

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data
Cited by: 29
Author(s): Michael Watson, Juliet Dukes, Abu-Bakr Abu-Median, Donald P. King, Paul Britton
Software Mentions: 5
Published: almost 18 years ago

10.1186/s12859-018-2299-7

CamurWeb: a classification software and a large knowledge base for gene expression data of cancer
Cited by: 9
Author(s): Emanuel Weitschek, Silvia Di Lauro, Eleonora Cappelli, Paola Bertolazzi, G. Felici
Software Mentions: 5
Published: about 6 years ago

10.1186/s12868-015-0217-8

Estimating the location and size of retinal injections from orthogonal images of an intact retina
Cited by: 3
Author(s): Johannes Hjorth, Élise Savier, David C. Sterratt, Michaël Reber, Stephen J. Eglen
Software Mentions: 5
Published: about 9 years ago

10.1186/1471-2105-12-35

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R
Cited by: 1,681
Author(s): Hanbo Chen, Paul C. Boutros
Software Mentions: 5
Published: almost 14 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: about 6 years ago

10.1007/s13205-016-0363-4

UpCoT: an integrated pipeline tool for clustering upstream DNA sequences of orthologous genes in prokaryotic genomes
Cited by: 0
Author(s): P. V. Parvati Sai Arun, Jogadhenu S. S. Prakash
Software Mentions: 5
Published: almost 9 years ago

10.1186/1471-2105-12-S1-S43

HDX-Analyzer: a novel package for statistical analysis of protein structure dynamics
Cited by: 34
Author(s): Sanmin Liu, Lantao Liu, Uğur Uzuner, Xin Zhou, Manxi Gu, Weibing Shi, Yixiang Zhang, Susie Y. Dai, Joshua S. Yuan
Software Mentions: 5
Published: almost 14 years ago

10.1186/1471-2105-10-391

JANE: efficient mapping of prokaryotic ESTs and variable length sequence reads on related template genomes
Cited by: 6
Author(s): Chunguang Liang, Alexander Schmid, María José López‐Sánchez, Andrés Moya, Roy Gross, Jörg Bernhardt, Thomas Dandekar
Software Mentions: 5
Published: about 15 years ago

10.1186/s13059-014-0577-x

Churchill: an ultra-fast, deterministic, highly scalable and balanced parallelization strategy for the discovery of human genetic variation in clinical and population-scale genomics
Cited by: 109
Author(s): Benjamin J. Kelly, James Fitch, Yangqiu Patrick Hu, Donald J. Corsmeier, Huachun Zhong, Amy Wetzel, Russell D Nordquist, David L. Newsom, Peter White
Software Mentions: 5
Published: almost 10 years ago

10.1016/j.celrep.2019.09.082

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data
Cited by: 120
Author(s): Erica A. K. DePasquale, Daniel Schnell, Pieter-Jan Van Camp, Íñigo Valiente-Alandí, Burns C. Blaxall, H. Leighton Grimes, Harinder Singh, Nathan Salomonis
Software Mentions: 5
Published: about 5 years ago

10.12688/f1000research.28142.2

MIREyA: a computational approach to detect miRNA-directed gene activation
Cited by: 1
Author(s): A. N. Elizarova, Mumin Ozturk, Reto Guler, Yulia A. Medvedeva
Software Mentions: 5
Published: over 3 years ago

10.1371/journal.pone.0091828

Characterization of Changes in Gene Expression and Biochemical Pathways at Low Levels of Benzene Exposure
Cited by: 36
Author(s): Reuben Thomas, Alan Hubbard, Cliona M. McHale, Luoping Zhang, Stephen M. Rappaport, Qing Lan, Nathaniel Rothman, Roel Vermeulen, Kathryn Z. Guyton, Jennifer Jinot, Babasaheb Sonawane, Martyn T. Smith
Software Mentions: 5
Published: over 10 years ago

10.1186/s40679-016-0035-9

Towards on-the-fly data post-processing for real-time tomographic imaging at TOMCAT
Cited by: 63
Author(s): Federica Marone, Alain Studer, Heiner Billich, L. Sala, Marco Stampanoni
Software Mentions: 5
Published: almost 8 years ago

10.12688/f1000research.21779.2

A role for MIR828 in pineapple fruit development
Cited by: 6
Author(s): Christopher D. Rock
Software Mentions: 5
Published: over 4 years ago

10.1186/1471-2105-7-64

HotSwap for bioinformatics: A STRAP tutorial
Cited by: 8
Author(s): Christoph Gille, Peter N. Robinson
Software Mentions: 5
Published: almost 19 years ago

10.1186/s40064-015-1356-1

Accurate mobile malware detection and classification in the cloud
Cited by: 26
Author(s): Xiaolei Wang, Yuexiang Yang, Yingzhi Zeng
Software Mentions: 5
Published: about 9 years ago

10.7717/peerj.3893

Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
Cited by: 49
Author(s): Ruth Timme, Hugh Rand, Martin Shumway, Eija Trees, Mustafa Simmons, Richa Agarwala, S. Scott Davis, Glenn E. Tillman, Stephanie Defibaugh-Chávez, Heather Carleton, William Klimke, Lee S. Katz
Software Mentions: 5
Published: about 7 years ago

10.1371/journal.pcbi.1008806

VolPy: Automated and scalable analysis pipelines for voltage imaging datasets
Cited by: 17
Author(s): Changjia Cai, Johannes Friedrich, Amrita Singh, M. Hossein Eybposh, Eftychios A. Pnevmatikakis, Kaspar Podgorski, Andrea Giovannucci
Software Mentions: 5
Published: over 3 years ago

10.1186/s12864-020-07183-9

A new method for long-read sequencing of animal mitochondrial genomes: application to the identification of equine mitochondrial DNA variants
Cited by: 7
Author(s): Sophie Dhorne–Pollet, Éric Barrey, Nicolas Pollet
Software Mentions: 5
Published: about 4 years ago

10.1371/journal.pone.0097277

GPU-BSM: A GPU-Based Tool to Map Bisulfite-Treated Reads
Cited by: 6
Author(s): Andrea Manconi, Alessandro Orro, Elias Manca, Giuliano Armano, Luciano Milanesi
Software Mentions: 5
Published: over 10 years ago

10.1371/journal.pone.0139868

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data
Cited by: 31
Author(s): Mohan A. V. S. K. Katta, Aamir W. Khan, Dadakhalandar Doddamani, Mahendar Thudi, Rajeev K. Varshney
Software Mentions: 5
Published: about 9 years ago

10.1155/2014/348725

Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics
Cited by: 6
Author(s): Anjani Ragothaman, Sairam Chowdary Boddu, Nayong Kim, Wei P. Feinstein, Michał Bryliński, Shantenu Jha, Joohyun Kim
Software Mentions: 4
Published: almost 11 years ago

10.1186/1745-6150-3-24

In silico regulatory analysis for exploring human disease progression
Cited by: 8
Author(s): Dustin T. Holloway, Mark A. Kon, Charles DeLisi
Software Mentions: 4
Published: over 16 years ago

10.1089/bio.2017.0014

Baobab Laboratory Information Management System: Development of an Open-Source Laboratory Information Management System for Biobanking
Cited by: 19
Author(s): Hocine Bendou, Lunga Sizani, Tim Reid, Carmen Swanepoel, Toluwaleke Ademuyiwa, Roxana Merino-Martinez, Heimo Meuller, Akin Abayomi, Alan Christoffels
Software Mentions: 4
Published: over 7 years ago

10.1186/1471-2105-12-27

CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes
Cited by: 25
Author(s): Franck Gauthier, O. C. Martin, Matthieu Falque
Software Mentions: 4
Published: almost 14 years ago

10.1371/journal.pone.0177459

Singularity: Scientific containers for mobility of compute
Cited by: 895
Author(s): Gregory M. Kurtzer, Vanessa Sochat, Michael Bauer
Software Mentions: 4
Published: over 7 years ago

10.1093/bioinformatics/btab178

PRISM: recovering cell-type-specific expression profiles from individual composite RNA-seq samples
Cited by: 13
Author(s): Antti Häkkinen, Kaiyang Zhang, Amjad Alkodsi, Noora Andersson, Erdoğan Pekcan Erkan, Jun Dai, Katja Kaipio, Tarja Lamminen, Naziha Mansuri, Kaisa Huhtinen, Anna Vähärautio, Olli Carpén, Johanna Hynninen, Sakari Hietanen, Rainer Lehtonen, Sampsa Hautaniemi
Software Mentions: 4
Published: almost 4 years ago

10.1371/journal.pone.0188511

Enhancing reproducibility in scientific computing: Metrics and registry for Singularity containers
Cited by: 33
Author(s): Vanessa Sochat, Cameron J. Prybol, Gregory M. Kurtzer
Software Mentions: 4
Published: about 7 years ago

10.1371/journal.pone.0098372

Maximal Sum of Metabolic Exchange Fluxes Outperforms Biomass Yield as a Predictor of Growth Rate of Microorganisms
Cited by: 9
Author(s): Raphy Zarecki, Matthew Oberhardt, Keren Yizhak, Allon Wagner, Ella Shtifman Segal, Shiri Freilich, Christopher S. Henry, Uri Gophna, Eytan Ruppin
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0081760

When Whole-Genome Alignments Just Won't Work: kSNP v2 Software for Alignment-Free SNP Discovery and Phylogenetics of Hundreds of Microbial Genomes
Cited by: 205
Author(s): Shea N. Gardner, Barry G. Hall
Software Mentions: 4
Published: about 11 years ago

10.1371/journal.pone.0100250

Novel Method for Analysis of Allele Specific Expression in Triploid Oryzias latipes Reveals Consistent Pattern of Allele Exclusion
Cited by: 8
Author(s): Tzintzuni Garcia, Isa Matos, Yingjia Shen, Vagmita Pabuwal, M. M. Coelho, Yuko Wakamatsu, Manfred Schartl, Ronald B. Walter
Software Mentions: 4
Published: over 10 years ago

10.1371/journal.pone.0246901

The analysis on the human protein domain targets and host-like interacting motifs for the MERS-CoV and SARS-CoV/CoV-2 infers the molecular mimicry of coronavirus
Cited by: 6
Author(s): Yamelie A. Martínez, Xianwu Guo, Diana Patricia Portales-Pérez, Gildardo Rivera, Julio Enrique Castañeda-Delgado, Carlos A. García-Pérez, José Antonio Enciso-Moreno, Edgar E. Lara-Ramírez
Software Mentions: 4
Published: almost 4 years ago

10.1186/s12889-021-11790-w

Electronic data collection, management and analysis tools used for outbreak response in low- and middle-income countries: a systematic review and stakeholder survey
Cited by: 4
Author(s): Patrick Keating, Jillian Murray, Karl Schenkel, Laura Merson, Anna C. Seale
Software Mentions: 4
Published: about 3 years ago

10.1186/s13059-015-0721-2

OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
Cited by: 2,420
Author(s): David Emms, Steven Kelly
Software Mentions: 4
Published: over 9 years ago

10.1186/gb-2008-9-1-r11

CPSARST: an efficient circular permutation search tool applied to the detection of novel protein structural relationships
Cited by: 36
Author(s): Wei-Cheng Lo, Ping Lyu
Software Mentions: 4
Published: almost 17 years ago

10.1186/1471-2105-8-462

Dynamic simulation of regulatory networks using SQUAD
Cited by: 137
Author(s): Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios, Luis Mendoza
Software Mentions: 4
Published: about 17 years ago

10.1371/journal.pcbi.1007453

TAPES: A tool for assessment and prioritisation in exome studies
Cited by: 15
Author(s): Alexandre Xavier, Rodney J. Scott, Bente A. Talseth‐Palmer
Software Mentions: 4
Published: about 5 years ago

10.1186/s13073-014-0125-z

Higher gene expression variability in the more aggressive subtype of chronic lymphocytic leukemia
Cited by: 51
Author(s): Simone Ecker, Véra Pancaldi, Daniel Rico, Alfonso Valencia
Software Mentions: 4
Published: almost 10 years ago

10.3389/fninf.2013.00039

Explicit B-spline regularization in diffeomorphic image registration
Cited by: 173
Author(s): Nicholas J. Tustison, Brian B. Avants
Software Mentions: 4
Published: almost 12 years ago

10.1186/1471-2105-11-598

Initial steps towards a production platform for DNA sequence analysis on the grid
Cited by: 8
Author(s): Angela C. M. Luyf, Barbera D.C. van Schaik, Michèl de Vries, Frank Baas, Antoine H. C. van Kampen, Sílvia D. Olabarriaga
Software Mentions: 4
Published: about 14 years ago

10.1186/s12859-016-1055-0

DensityMap: a genome viewer for illustrating the densities of features
Cited by: 13
Author(s): Sébastien Guizard, Benoît Piégu, Yves Bigot
Software Mentions: 4
Published: over 8 years ago

10.1371/journal.pcbi.1009411

ISOTOPE: ISOform-guided prediction of epiTOPEs in cancer
Cited by: 5
Author(s): Juan L. Trincado, Marina Reixachs‐Solé, Judith Pérez-Granado, Tim Fugmann, Ferrán Sanz, Jun Yokota, Eduardo Eyras
Software Mentions: 4
Published: over 3 years ago

10.3389/fpsyt.2019.00280

Transcriptome Changes in Relation to Manic Episode
Cited by: 15
Author(s): Ya Chin Lee, Yu Chao, Chiao-Erh Chang, Ming H. Hsieh, Kuan‐Ting Liu, Hsi‐Chung Chen, Mong Liang Lu, Wen Yin Chen, Chun Hsin Chen, Meng-Tsan Tsai, Tzu-Pin Lu, Ming Huang, Po-Hsiu Kuo
Software Mentions: 4
Published: over 5 years ago

Projects: pypi: linux

Papers Mentioning linux 450