Galaxy: A platform for interactive large-scale genome analysis

Giardine, Belinda; Riemer, Cathy; Hardison, Ross C.; Burhans, Richard; Elnitski, Laura; Shah, Prachi; Zhang, Yi; Blankenberg, Daniel; Albert, István; Taylor, James G.; Miller, Webb; Kent, W. James; Nekrutenko, Anton

doi:10.1101/gr.4086505

Cited by 1,831 publications

(1,432 citation statements)

References 25 publications

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“…These examples were chosen to showcase edgeR’s ability to deal with experiments of varying size (from tens to thousands of hairpins) and complexity, from two-group situations, to settings with four groups, or a time-course design, where a GLM with a slope and intercept term is most appropriate. We have also developed a Galaxy tool 15– 17 that implements this workflow as a point-and-click application to improve accessibility for researchers who are unfamiliar with the R programming environment ( Figure 2). …”

Section: Methodsmentioning

confidence: 99%

shRNA-seq data analysis with edgeR

et al. 2014

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Pooled short hairpin RNA sequencing (shRNA-seq) screens are becoming increasingly popular in functional genomics research, and there is a need to establish optimal analysis tools to handle such data. Our open-source shRNA processing pipeline in edgeR provides a complete analysis solution for shRNA-seq screen data, that begins with the raw sequence reads and ends with a ranked lists of candidate shRNAs for downstream biological validation. We first summarize the raw data contained in a fastq file into a matrix of counts (samples in the columns, hairpins in the rows) with options for allowing mismatches and small shifts in hairpin position. Diagnostic plots, normalization and differential representation analysis can then be performed using established methods to prioritize results in a statistically rigorous way, with the choice of either the classic exact testing methodology or a generalized linear modelling that can handle complex experimental designs. A detailed users’ guide that demonstrates how to analyze screen data in edgeR along with a point-and-click implementation of this workflow in Galaxy are also provided. The edgeR package is freely available from http://www.bioconductor.org.

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Section: Methodsmentioning

confidence: 99%

shRNA-seq data analysis with edgeR

et al. 2014

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“…Richness estimators, diversity indices and coverage percentage were calculated from randomly subsampled set of sequences (based on the smallest dataset) in mothur. To visualize the number and correlation of taxa at different taxonomic ranks among samples, CoVennTree (Lott et al, 2015) was used, a tool on the Galaxy platform (Giardine et al, 2005;Blankenberg et al, 2010;Goecks et al, 2010). The resulted output was visualized in Cytoscape 2.8.3 (Shannon et al, 2003).…”

Section: Pyrosequencingmentioning

confidence: 99%

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Borsodi

Krett

Felföldi

et al. 2017

Microbiological Research

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Studying the microbiota in the alimentary tract of bigheaded carps (Hypophthalmichthys spp.) gained special interest recently, as these types of investigations on non-native fish species may lead to a better understanding of their ecological role and feeding habits in an invaded habitat. For microbiological examinations, bigheaded carp gut contents and water column samples from Lake Balaton (Hungary) were collected from spring to autumn in 2013.Denaturing Gradient Gel Electrophoresis (DGGE) and pyrosequencing of the 16S rRNA gene were performed to reveal the composition. According to the DGGE patterns, bacterial communities of water samples separated clearly from that of the intestines. Moreover, the bacterial communities in the foreguts and hindguts were also strikingly dissimilar. Based on pyrosequencing, both foregut and hindgut samples were predominated by the fermentative genus Cetobacterium (Fusobacteria). The presence of some phytoplankton taxa and the high relative abundance of cellulose-degrading bacteria in the guts suggest that intestinal microbes may have an important role in digesting algae and making them utilizable for bigheaded carps that lack cellulase enzyme. In turn, the complete absence of typical heterotrophic freshwater bacteria in all studied sections of the intestines indicated that bacterioplankton probably has a negligible role in the nutrition of bigheaded carps.

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“…We then describe their practical implementation using tools on the Galaxy platform (www.galaxyproject.org) [29]. Our tools are available at http://galaxy-chen.cnsi.ucsb.edu:8080/.…”

Section: Methodsmentioning

confidence: 99%

“…We implemented our methods using the Galaxy bioinformatics platform [29]. Before using our tools, any paired end FASTQ data should be joined and groomed, and any reverse complements should be converted to align with the expected sequencing output.…”

Section: Practical Implementationmentioning

confidence: 99%

Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments

Xulvi-Brunet

Campbell

Rajamani

et al. 2016

Methods

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In vitro selection experiments in biochemistry allow for the discovery of novel molecules capable of specific desired biochemical functions. However, this is not the only benefit we can obtain from such selection experiments. Since selection from a random library yields an unprecedented, and sometimes comprehensive, view of how a particular biochemical function is distributed across sequence space, selection experiments also provide data for creating and analyzing molecular fitness landscapes, which directly map function (phenotypes) to sequence information (genotypes). Given the importance of understanding the relationship between sequence and functional activity, reliable methods to build and analyze fitness landscapes are needed. Here, we present some statistical methods to extract this information from pools of RNA molecules. We also provide new computational tools to construct and study molecular fitness landscapes.

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Galaxy: A platform for interactive large-scale genome analysis

Cited by 1,831 publications

References 25 publications

shRNA-seq data analysis with edgeR

shRNA-seq data analysis with edgeR

Gut content microbiota of introduced bigheaded carps ( Hypophthalmichthys spp.) inhabiting the largest shallow lake in Central Europe

Computational analysis of fitness landscapes and evolutionary networks from in vitro evolution experiments

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