tag:joss.theoj.org,2005:/papers/edited_by/@will-rowe?page=1
Journal of Open Source Software
2021-12-24T16:41:35Z
Journal of Open Source Software
https://joss.theoj.org
tag:joss.theoj.org,2005:Paper/3110
2021-12-24T16:41:35Z
2021-12-25T00:01:13Z
Sepia, a taxonomy oriented read classifier in Rust
accepted
v0.0.2
2021-10-14 16:38:44 UTC
68
2021-12-24 16:41:35 UTC
6
2021
3839
Henk
C. den
Bakker
Center for Food Safety, University of Georgia, Griffin, GA, USA
0000-0002-4086-1580
Lee
S.
Katz
Center for Food Safety, University of Georgia, Griffin, GA, USA, Enteric Diseases Laboratory Branch (EDLB), Centers for Disease Control and Prevention, Atlanta, GA, USA
0000-0002-2533-9161
10.21105/joss.03839
https://doi.org/10.5281/zenodo.5787248
Python, Rust
https://joss.theoj.org/papers/10.21105/joss.03839.pdf
read classification, taxonomy
tag:joss.theoj.org,2005:Paper/3119
2021-11-17T10:05:14Z
2021-11-18T00:02:22Z
Microbiome.jl and BiobakeryUtils.jl - Julia packages for working with microbial community data
accepted
v0.8.0
2021-10-20 19:33:59 UTC
67
2021-11-17 10:05:14 UTC
6
2021
3876
Kevin
S.
Bonham
Department of Biological Sciences, Wellesley College
Annelle
Abatoni
Kayisire
Department of Biological Sciences, Wellesley College
Anika
S.
Luo
Department of Biological Sciences, Wellesley College
Vanja
Klepac-Ceraj
Department of Biological Sciences, Wellesley College
10.21105/joss.03876
https://doi.org/10.5281/zenodo.5682344
Julia
https://joss.theoj.org/papers/10.21105/joss.03876.pdf
julia, biology, microbiome, microbial communities
tag:joss.theoj.org,2005:Paper/2561
2021-06-10T14:52:39Z
2021-06-11T00:01:28Z
Eir: A Python Package for Epidemic Simulation
accepted
v 0.1.20
2021-04-09 03:01:41 UTC
62
2021-06-10 14:52:39 UTC
6
2021
3247
Mathew
Jacob
RxCovea, New York University, New York, USA
0000-0001-5513-432X
10.21105/joss.03247
https://doi.org/10.5281/zenodo.4905077
Python
https://joss.theoj.org/papers/10.21105/joss.03247.pdf
epidemiology, super spreaders, spatial models, stochastic
tag:joss.theoj.org,2005:Paper/2139
2021-01-08T09:10:54Z
2021-02-15T11:29:47Z
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes
accepted
v1.0.0
2020-10-29 10:55:19 UTC
57
2021-01-08 09:10:54 UTC
6
2021
2817
Arianna
I.
Krinos
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, MIT-WHOI Joint Program in Oceanography, Cambridge and Woods Hole, MA, USA
0000-0001-9767-8392
Sarah
K.
Hu
Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA, Center for Dark Energy Biosphere Investigations, University of Southern California, Los Angeles, CA, USA
0000-0002-4439-1360
Natalie
R.
Cohen
Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
0000-0001-6156-9186
Harriet
Alexander
Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA, USA
0000-0003-1308-8008
10.21105/joss.02817
https://doi.org/10.5281/zenodo.4422091
Python
https://joss.theoj.org/papers/10.21105/joss.02817.pdf
Taxonomy, Metagenomics, Metatranscriptomics
tag:joss.theoj.org,2005:Paper/1830
2020-10-12T19:51:22Z
2021-02-15T11:30:20Z
CPgeneProfiler: A lightweight R package to profile the Carbapenamase genes from genome assemblies
accepted
v2.1.0
2020-07-06 08:33:06 UTC
54
2020-10-12 19:51:22 UTC
5
2020
2473
Prakki
Sai Rama
Sridatta
National Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore
0000-0002-9254-2557
Natascha
M.
Thevasagayam
National Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore
Weizhen
Xu
National Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore
Kalisvar
Marimuthu
National Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore
Jeanette
W p
Teo
National University Hospital, Singapore
Indumathi
Venkatachalam
Singapore General Hospital, Singapore
Ng
Oon
Tek
National Centre for Infectious Diseases, Singapore, Tan Tock Seng Hospital, Singapore, Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
10.21105/joss.02473
https://doi.org/10.5281/zenodo.4076089
R
https://joss.theoj.org/papers/10.21105/joss.02473.pdf
Carbapenamase gene profile, cocarriage, Beta-lactamases, Antimicrobial resistance (AMR)
tag:joss.theoj.org,2005:Paper/1811
2020-09-23T23:57:46Z
2022-01-18T11:38:56Z
Chromatiblock: scalable whole-genome visualization of structural differences in prokaryotes
accepted
v0.4.2
2020-07-01 04:17:07 UTC
53
2020-09-23 23:57:46 UTC
5
2020
2451
Mitchell
John
Sullivan
Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
Harm
van Bakel
Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States of America
10.21105/joss.02451
https://doi.org/10.5281/zenodo.4034604
Python
https://joss.theoj.org/papers/10.21105/joss.02451.pdf
Bioinformatics, Microbial genomics, Visualization, multiple alignment
tag:joss.theoj.org,2005:Paper/1698
2020-07-10T20:10:24Z
2021-02-15T11:30:36Z
COVID-19 Data Hub
accepted
2.0.7
2020-05-28 19:34:46 UTC
51
2020-07-10 20:10:24 UTC
5
2020
2376
Emanuele
Guidotti
University of Neuchâtel, Switzerland
0000-0002-8961-6623
David
Ardia
HEC Montréal, Canada
0000-0003-2823-782X
10.21105/joss.02376
https://doi.org/10.5281/zenodo.3939184
R
https://joss.theoj.org/papers/10.21105/joss.02376.pdf
COVID-19
tag:joss.theoj.org,2005:Paper/1418
2020-05-12T11:01:32Z
2021-02-15T11:31:12Z
Recan: Python tool for analysis of recombination events in viral genomes
accepted
v0.1
2019-12-20 09:02:51 UTC
49
2020-05-12 11:01:32 UTC
5
2020
2014
Yuriy
Babin
National Medical Research Center for Tuberculosis and Infectious Diseases, Moscow, Russia
0000-0002-7524-5921
10.21105/joss.02014
https://doi.org/10.5281/zenodo.3820660
Python
https://joss.theoj.org/papers/10.21105/joss.02014.pdf
virology, recombination
tag:joss.theoj.org,2005:Paper/1439
2020-04-26T12:39:35Z
2021-02-15T11:31:09Z
scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data
accepted
0.0.5
2020-01-14 14:41:38 UTC
48
2020-04-26 12:39:35 UTC
5
2020
2061
J.
Sebastian
Paez
Purdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology
0000-0002-0065-1474
Michael
K.
Wendt
Purdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology
0000-0002-3665-7413
Nadia
Atallah
Lanman
Purdue University, Center for Cancer Research, Purdue University, Department of Comparative Pathobiology
0000-0002-1819-7070
10.21105/joss.02061
https://doi.org/10.5281/zenodo.3766467
R
https://joss.theoj.org/papers/10.21105/joss.02061.pdf
Bioinformatics, Single cell, Flow Cytometry
tag:joss.theoj.org,2005:Paper/1461
2020-03-06T17:24:08Z
2021-02-15T11:31:05Z
covtobed: a simple and fast tool to extract coverage tracks from BAM files
accepted
v1.0.0
2020-01-30 15:43:55 UTC
47
2020-03-06 17:24:08 UTC
5
2020
2119
Giovanni
Birolo
Dept. Medical Sciences, University of Turin, ITALY
Andrea
Telatin
Gut Microbes and Health Programme, Quadram Institute Bioscience, Norwich, UK
0000-0001-7619-281X
10.21105/joss.02119
https://doi.org/10.5281/zenodo.3695204
C++
https://joss.theoj.org/papers/10.21105/joss.02119.pdf
bedtools, bamtools, genomics, bioinformatics, target enrichment, sequence coverage