tag:joss.theoj.org,2005:/papers/tagged/rna-seqJournal of Open Source Software2022-06-01T13:40:28ZJournal of Open Source Softwarehttps://joss.theoj.orgtag:joss.theoj.org,2005:Paper/33852022-06-01T13:40:28Z2022-06-02T00:01:05ZMitoHEAR: an R package for the estimation and downstream statistical analysis of the mitochondrial DNA heteroplasmy calculated from single-cell datasetsacceptedv1.0.02022-02-21 11:28:37 UTC742022-06-01 13:40:28 UTC720224265GabrieleLubattiInstitute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany, Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, GermanyElmirMahammadovInstitute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany, Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, GermanyAntonioScialdoneInstitute of Epigenetics and Stem Cells, Helmholtz Zentrum München, Munich, Germany, Institute of Functional Epigenetics, Helmholtz Zentrum München, Neuherberg, Germany, Institute of Computational Biology, Helmholtz Zentrum München, Neuherberg, Germany10.21105/joss.04265https://doi.org/10.5281/zenodo.6598821Rhttps://joss.theoj.org/papers/10.21105/joss.04265.pdfbioinformatics, single cell RNA seq, heteroplasmytag:joss.theoj.org,2005:Paper/14142020-08-31T06:20:10Z2021-02-15T11:31:13ZNEEP: null empirically estimated p-values for high-throughput molecular survival analysisacceptedv12019-12-19 17:26:54 UTC522020-08-31 06:20:10 UTC520202044SeanWestSchool of Interdisciplinary Informatics, University of Nebraska at Omaha0000-0002-1394-1999HeshamAliSchool of Interdisciplinary Informatics, University of Nebraska at OmahaDarioGhersiSchool of Interdisciplinary Informatics, University of Nebraska at Omaha0000-0002-0630-084310.21105/joss.02044https://doi.org/10.5281/zenodo.3996816C++, Chttps://joss.theoj.org/papers/10.21105/joss.02044.pdfPython, bioinformatics, survival analysis, RNA-seqtag:joss.theoj.org,2005:Paper/13252019-11-17T16:16:31Z2021-02-15T11:31:23Zrnassqs: An R package to access agricultural data via the USDA National Agricultural Statistics Service (USDA-NASS) 'Quick Stats' APIacceptedv0.6.12019-11-08 00:07:06 UTC432019-11-17 16:16:31 UTC420191880NicholasA.PotterWashington State University0000-0002-3410-373210.21105/joss.01880https://doi.org/10.5281/zenodo.3532167Rhttps://joss.theoj.org/papers/10.21105/joss.01880.pdfAPI, reproducibility, agriculture, economicstag:joss.theoj.org,2005:Paper/11442019-08-05T11:48:32Z2021-02-15T11:31:50ZThe UCSCXenaTools R package: a toolkit for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seqacceptedv1.2.52019-08-02 09:49:13 UTC402019-08-05 11:48:32 UTC420191627ShixiangWangSchool of Life Science and Technology, ShanghaiTech University, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences0000-0001-9855-7357XuesongLiuSchool of Life Science and Technology, ShanghaiTech University0000-0002-7736-007710.21105/joss.01627https://doi.org/10.5281/zenodo.3358530R, XQueryhttps://joss.theoj.org/papers/10.21105/joss.01627.pdfcancer genomics, data accesstag:joss.theoj.org,2005:Paper/9332019-07-07T15:58:35Z2021-02-15T11:32:23ZGUESSmyLT: Software to guess the RNA-Seq library type of paired and single end read filesacceptedv1.02019-03-19 10:22:25 UTC392019-07-07 15:58:35 UTC420191344ErikBernerWikMolecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.HampusOlinMolecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.CaitlinVigetunHaugheyMolecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.LisaKlassonMolecular Evolution, Department of Cell and Molecular Biology, Uppsala University, 75124 Sweden.JacquesDainatIMBIM - Department of Medical Biochemistry and Microbiology, Box 582, S-751 23 Uppsala, SWEDEN., National Bioinformatics Infrastructure Sweden (NBIS), SciLifeLab, Uppsala Biomedicinska Centrum (BMC), Husargatan 3, S-751 23 Uppsala, SWEDEN.0000-0002-6629-017310.21105/joss.01344https://doi.org/10.5281/zenodo.3268394Pythonhttps://joss.theoj.org/papers/10.21105/joss.01344.pdfRNA-seq, library-typetag:joss.theoj.org,2005:Paper/8372019-05-01T00:45:47Z2021-02-15T11:32:35ZCompare Expression Profiles for Pre-defined Gene Groups with C-RExacceptedv1.02019-01-28 18:01:49 UTC372019-05-01 00:45:47 UTC420191255MingzeHeBioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA, 50011, Department of Agronomy, Iowa State University, Ames, Iowa, USA 500110000-0002-8164-2480KokulapalanWimalanathanBioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA, 50011, Department of Agronomy, Iowa State University, Ames, Iowa, USA 500110000-0001-7811-935XPengLiuBioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA, 50011, Department of Agronomy, Iowa State University, Ames, Iowa, USA 500110000-0002-2093-8018CarolynJ.Lawrence-DillBioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA, 50011, Department of Agronomy, Iowa State University, Ames, Iowa, USA 50011, Department of Agronomy, Iowa State University, Ames, Iowa, USA 500110000-0003-0069-143010.21105/joss.01255https://doi.org/10.5281/zenodo.2651751Rhttps://joss.theoj.org/papers/10.21105/joss.01255.pdfGene Group, RNA-seq, Shiny, Normalization, Statistics test, Visualizationtag:joss.theoj.org,2005:Paper/7522019-02-17T16:40:34Z2021-02-15T11:32:44ZstrandCheckR: An R package for quantifying and removing double strand sequences for strand-specific RNA-seqaccepted1.0.02018-12-14 12:37:09 UTC342019-02-17 16:40:34 UTC420191145Thu-HienToBioinformatics Hub - University of Adelaide0000-0003-2902-3655StephenM.PedersonBioinformatics Hub - University of Adelaide0000-0001-8197-330310.21105/joss.01145https://doi.org/10.5281/zenodo.2555032Rhttps://joss.theoj.org/papers/10.21105/joss.01145.pdfBioinformatics, RNA-seq, strand specific, DNA contaminationtag:joss.theoj.org,2005:Paper/3762018-08-27T12:36:32Z2021-02-15T11:33:38ZRNAsik: A Pipeline for complete and reproducible RNA-seq analysis that runs anywhere with speed and easeaccepted1.4.92018-02-07 23:07:43 UTC282018-08-27 12:36:32 UTC32018583KirillTsyganovMonash Bioinformatics Platform, Monash University0000-0002-9195-2626AndrewJamesPerryMonash Bioinformatics Platform, Monash University0000-0001-9256-6068StuartKennethArcherMonash Bioinformatics Platform, Monash University0000-0003-0450-1243DavidPowellMonash Bioinformatics Platform, Monash University0000-0002-6639-625010.21105/joss.00583https://doi.org/10.5281/zenodo.1403976C, Pythonhttps://joss.theoj.org/papers/10.21105/joss.00583.pdfRNA-seq, gene expression, pipeline, bioinformaticstag:joss.theoj.org,2005:Paper/2432017-08-30T00:00:00Z2021-02-15T11:34:00Z'Sequana': a Set of Snakemake NGS pipelinesaccepted0.4.12017-07-24 11:05:35 UTC162017-08-30 00:00:00 UTC22017352ThomasCokelaerInstitut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France, Institut Pasteur - Biomics Pole - Paris, France0000-0001-6286-1138DimitriDesvillechabrolInstitut Pasteur - Biomics Pole - Paris, France0000-0002-4947-7876RachelLegendreInstitut Pasteur - Bioinformatics and Biostatistics Hub - C3BI, USR 3756 IP CNRS - Paris, France, Institut Pasteur - Biomics Pole - Paris, France0000-0002-5196-9431MélissaCardonInstitut Pasteur - Biomics Pole - Paris, France0000-0001-9906-323610.21105/joss.00352https://doi.org/10.5281/zenodo.853160Jupyter Notebook, Pythonhttps://joss.theoj.org/papers/10.21105/joss.00352.pdfsnakemake, rna-seq, variant calling, taxonomy, denovo, pipeline, genome coveragetag:joss.theoj.org,2005:Paper/1702017-08-27T00:00:00Z2021-02-15T11:34:12ZVaristran: Anscombe's variance stabilizing transformation for RNA-seq gene expression dataacceptedv1.0.12017-03-13 04:38:01 UTC162017-08-27 00:00:00 UTC22017257PaulFrancisHarrisonMonash Bioinformatics Platform, Monash University0000-0002-3980-268X10.21105/joss.00257https://doi.org/10.5281/zenodo.846925Rhttps://joss.theoj.org/papers/10.21105/joss.00257.pdfRNA-seq, gene expression, variance stabilizing transformation, R package