RobiNA protocols

View RobiNA computational protocol

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RobiNA specifications

Information


Unique identifier OMICS_01411
Name RobiNA
Software type Pipeline/Workflow
Interface Graphical user interface
Restrictions to use None
Input format FASTQ
Output format PDF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, R
License GNU General Public License version 3.0, GNU Lesser General Public License version 3.0
Computer skills Medium
Version 1.2.4
Stability Stable
Requirements
Bowtie, EdgeR, DeSeq
Maintained Yes

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Maintainer


  • person_outline Marc Lohse <>

Publication for RobiNA

RobiNA in pipelines

 (4)
2018
PMCID: 5862806
PMID: 29599762
DOI: 10.3389/fmicb.2018.00472

[…] in at least one of the strains. de genes were those with a fold change of at least 2, and fdr lower than 0.05. for the second de analysis, the read counts table was exported from clc into the robina software () and statistical evaluation of differential gene expression was performed by deseq () considering a p-value cut-off of 0.05 using the benjamini–hochberg method for multiple testing […]

2017
PMCID: 5312494
PMID: 28229116
DOI: 10.1016/j.dib.2017.02.008

[…] than 2 bases were permitted. differential gene expression between water and ja-treated roots at 2 d post-treatment and between water and ja-treated roots at 60 d post-treatment were determined using robina software . only unigenes with an absolute value of log2 (fold change) ≥1 and a false discovery rate (fdr) ≤0.001 were considered differentially expressed. annotations to the sugarbeet genome […]

2014
PMCID: 4238952
PMID: 25411840
DOI: 10.1371/journal.pgen.1004806

[…] wild type comparison when the benjamini-hochberg's fdr was <0.1 and the log2 fold change was >1 or <−1. raw genechip arabidopsis ath1 genome array (affymetrix) data were analyzed with the robina software and the probesets were considered differentially changed by the heat treatment using the above parameters. the non-redundant functional categories of the differentially changed […]

2013
PMCID: 3759049
PMID: 23996052
DOI: 10.1038/srep02544

[…] 4 system (life technologies)., the reads were mapped against the h. seropedicae smr1 genome (nc_014323) as reference using the clc genomics workbench package. read counts table was exported into the robina software and both normalization and statistical evaluation of differential gene expression was performed by deseq with a p-value cut-off of 0.05 using the benjamini-hochberg method […]


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RobiNA in publications

 (36)
PMCID: 5827775
PMID: 29520310
DOI: 10.3762/bjoc.14.34

[…] the change in fluorescence of tryptophan-88, located in the gm1 binding site, upon titration of the protein with the inhibitor. compound 6 showed excellent binding with a k d value of 23 µm []. robina and co-workers synthesised non-hydrolyzable s-galactosides and non-carbohydrate ligands based on polyhydroxyalkylfuronate moieties and measured their affinities by weak affinity chromatography […]

PMCID: 5749873
PMID: 29253890
DOI: 10.1371/journal.pgen.1007132

[…] publicly available microarray data was downloaded from gene expression omnibus (gse39385, gse5727, gse19255, gse10646, gse5632) and arrayexpress (e-mexp-173, e-mexp-1474) [,,,,,] and reanalyzed with robina using the plier algorithm []., various strains of pseudomonas syringae pv. tomato strain dc3000 were grown on king’s b plates for 2–3 days at room temperature. needless syringe infiltration […]

PMCID: 5691830
PMID: 29145869
DOI: 10.1186/s12955-017-0797-3

[…] can promote these strategies in work with others in effort to keep qol as positive as possible., the authors wish to thank study participants for their contributions to this research and the robina foundation for their support of the lifecourse study., the lifecourse study is funded by the robina foundation., the datasets used and/or analyzed during the current study are available […]

PMCID: 5644101
PMID: 29075312
DOI: 10.1186/s13007-017-0236-9

[…] gsa wrote the paper: aak, aa, amn, ae, sb, za, djn and gsa. revised and approved the final version of the paper: gsa. all authors read and approved the final manuscript. , we thank mary brennan and robina ali for growing plants and isolating dna plasmids., the authors declare that they have no competing interests., not applicable., not applicable., not applicable., this work was supported […]

PMCID: 5602955
PMID: 28915789
DOI: 10.1186/s12864-017-4126-3

[…] rna samples processed was 21, comprising three independent biological replicates of each of the seven conditions described above., the raw arabidopsis gene 1.0 st intensities were imported into the robina software [] to perform quality assessment and data normalization and to identify genes differentially regulated between cold acclimated plants and plants subjected to different durations […]


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RobiNA institution(s)
Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany; RWTH Aachen University, Aachen, Germany; Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Julich, Germany
RobiNA funding source(s)
Supported by the German Ministry of Education and Research (BMBF) [project 0315912].

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