ReadXplorer statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Read alignment visualization chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

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


Add your version

Maintainer


  • person_outline Rolf Hilker <>

Publication for ReadXplorer

ReadXplorer in pipelines

 (8)
2018
PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] genome of g. oxydans using bowtie2 v2.2.7 [, ]. cufflinks and cuffnorm were used to quantify transcript levels []., detection of tsss was done with libraries enriched for primary transcripts using readxplorer [] with the following parameters: (i) only single perfect mappings were considered. (ii) minimum percent of coverage increase was set to 250% and minimum number of read starts to 20. […]

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

[…] 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 []., the analysis of the primary 5′-end cdna data with the software readxplorer [] resulted in the automatic detection of 3987 putative transcription start sites (tss) in the c. […]

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

[…] 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 […]

2017
PMCID: 5423683
PMID: 28486484
DOI: 10.1371/journal.pone.0177278

[…] –ln679996] using tophat2 []. two mismatches were allowed to account for possible sequencing errors and allelic variants of the diploid r. solani ag1-ib genome []. the rna-seq analysis platform readxplorer [] was used for the visualization of short read alignments., results of the short read mapping were imported into the platform readxplorer 2.0.1. [,]. the r package deseq [] was selected […]

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

[…] sequencing errors and the read length of 50 bp, up to two mismatches were allowed in mapping. expression analysis and visualization was performed by using the short-read mapping analysis platform readxplorer 2.2.3 []., the readxplorer platform also includes the r package deseq [–], which was used to normalize the count data and calculate mean values (basemean, basemeana, basemeanb), fold […]


To access a full list of citations, you will need to upgrade to our premium service.

ReadXplorer in publications

 (21)
PMCID: 5958101
PMID: 29773797
DOI: 10.1038/s41467-018-04364-9

[…] 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 […]

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

[…] default settings for single-end read mapping. all mapped sequence data was converted from sam to bam format to decrease usage of disk space with samtools v1.3 [] and visualized and inspected with readxplorer v.2.2 []., to automatically detect transcription start sites (tss), the tss detection mode of the ‘transcription analyses’ function of readxplorer was applied on the primary 5′-end cdna […]

PMCID: 5756330
PMID: 29304737
DOI: 10.1186/s12864-017-4415-x

[…] transcripts. all automatically detected tsss were checked manually and tsss without a clear read start increase and unusual drops or increase of read coverage were removed., the tsss identified by readxplorer were classified according to the following categories allowing the occurrence of some tss in more than one category (fig. ): (a) tsss assigned to an annotated orf in sense orientation […]

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

[…] 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% […]

PMCID: 5698495
PMID: 29181449
DOI: 10.1128/mSystems.00141-17

[…] of the novel transcripts in males and females, and the putative functions of these transcripts are unknown., potential novel ceper1 transcripts and putative antisense rnas, calculated with readxplorer. the parameter “number of read starts” counts the number of reads and filters low-coverage regions with a number of reads below a certain threshold. the threshold used to detect novel […]


To access a full list of publications, you will need to upgrade to our premium service.

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

ReadXplorer reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review ReadXplorer