ReadXplorer statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ReadXplorer
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Tool usage distribution map

This map represents all the scientific publications referring to ReadXplorer per scientific context
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Associated diseases

This word cloud represents ReadXplorer usage per disease context
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Protocols

ReadXplorer specifications

Information


Unique identifier OMICS_04011
Name ReadXplorer
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Rolf Hilker

Publication for ReadXplorer

ReadXplorer citations

 (19)
library_books

Three previously unrecognised classes of biosynthetic enzymes revealed during the production of xenovulene A

2018
Nat Commun
PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] (non-production) media and sequenced by standard Illumina methods. Tophat2 was used to map quality-filtered reads onto the S. schorii draft genome. Differential gene expression was then analysed with ReadXplorer 2.0 including the DESeq package. The results (Fig. ) clearly show that genes from asL7 to asR7, inclusive, are significantly upregulated under producing conditions, while genes outwith thi […]

library_books

Transcriptome sequencing of the human pathogen Corynebacterium diphtheriae NCTC 13129 provides detailed insights into its transcriptional landscape and into DtxR mediated transcriptional regulation

2018
BMC Genomics
PMCID: 5784534
PMID: 29370758
DOI: 10.1186/s12864-018-4481-8

[…] using default parameters. Between 96 to 99% of the reads were mapped to the genomic reference (Additional file : Table S2). For visualization and further analysis, the mapped reads were imported into ReadXplorer []. […]

library_books

Whole transcriptome RNA Seq analysis reveals extensive cell type specific compartmentalization in Volvox carteri

2017
BMC Biol
PMCID: 5704591
PMID: 29179763
DOI: 10.1186/s12915-017-0450-y

[…] reads from reproductive cells. Thus, both cell types contributed the same number of mapped reads.Expression analysis and visualization was performed by using the short-read mapping analysis platform ReadXplorer 2.2.3 []. The mapped reads hit 14,203 out of the 14,247 predicted genes of the V. carteri genome (annotation v2.1) on the Phytozome V12 platform [], which corresponds to 99.7% of all predi […]

call_split

Transcriptome Sequencing Reveals Novel Candidate Genes for Cardinium hertigii Caused Cytoplasmic Incompatibility and Host Cell Interaction

2017
mSystems
PMCID: 5698495
PMID: 29181449
DOI: 10.1128/mSystems.00141-17
call_split See protocol

[…] then verified by manual searches of proteins against Swiss-Prot and UniProt, as well as searches against PFAM and SMART (see reference for details). Read counts per predicted gene were calculated by ReadXplorer () and imported in DESeq Bioconductor using the R software environment (). Gene counts were normalized to size factors of libraries and dispersion estimation. Normalized gene expression va […]

library_books

Detailed transcriptome analysis of the plant growth promoting Paenibacillus riograndensis SBR5 by using RNA seq technology

2017
BMC Genomics
PMCID: 5670726
PMID: 29100491
DOI: 10.1186/s12864-017-4235-z

[…] To determine and classify the TSS based on mapped 5′-end enriched RNA-seq data, we used the software for visualization of mapped sequences ReadXplorer []. This determination was done in 2 steps, automatic TSS determination and manual data set curing. First, the TSS were automatically detected by ReadXplorer Transcription Analysis Paramet […]

library_books

The transcriptional regulator LysG (Rv1985c) of Mycobacterium tuberculosis activates lysE (Rv1986) in a lysine dependent manner

2017
PLoS One
PMCID: 5648196
PMID: 29049397
DOI: 10.1371/journal.pone.0186505

[…] e (www.ebi.ac.uk/arrayexpress) [] under Accession No.: E-MTAB-6011. Reads were mapped onto the genomic reference sequence of Mycobacterium tuberculosis H37Rv with Bowtie 2 [] using standard settings. ReadXplorer 2.2.0 [] was used for visualization of short read alignments and data analysis including transcript start site determination. […]


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ReadXplorer institution(s)
Bioinformatics and Systems Biology, Faculty of Biology and Chemistry, Justus-Liebig-University, Giessen, Germany

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