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add new tools links
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@pavanvidem
pavanvidem committed Feb 7, 2019
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Expand Up @@ -36,7 +36,7 @@ De novo transcriptome reconstruction with RNA-Seq | | [<i class="fa fa-laptop"
Differential abundance testing of small RNAs | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/srna/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/826906){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=7734928ebc0a2654){:target="_blank"} [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=1ffc058273ab357e){:target="_blank"} | [<i class="fa fa-magic" aria-hidden="true"></i>]({{ page.website }}/tours/differential_abundance_testing_sRNAs){:target="_blank"} |
Network analysis with Heinz | [<i class="fa fa-slideshare" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/slides.html){:target="_blank"} | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/network-analysis-with-heinz/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/1344105){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=12c80c5b5e2305d8){:target="_blank"} | [<i class="fa fa-magic" aria-hidden="true"></i>]({{ page.website }}/tours/network-analysis-with-heinz){:target="_blank"} | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-workbench-network-analysis-with-heinz){:target="_blank"}
PAR-CLIP analysis | | | [<i class="fa fa-files-o" aria-hidden="true"></i>](http://doi.org/10.5281/zenodo.2553519){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=a108b575b16e6cb9){:target="_blank"} | | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/joerg-fallmann/h/parclipworkflow){:target="_blank"}
Reference-based RNA-Seq data analysis | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/1185122){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=9c7a218993788493){:target="_blank"} | [<i class="fa fa-magic" aria-hidden="true"></i>]({{ page.website }}/tours/ref_based_rna-seq){:target="_blank"} |
Reference-based RNA-Seq data analysis | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/ref-based/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/1185122){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=9c7a218993788493){:target="_blank"} | [<i class="fa fa-magic" aria-hidden="true"></i>]({{ page.website }}/tours/ref_based_rna-seq){:target="_blank"} | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/andrea.bagnacani/h/reference-based-rna-seq){:target="_blank"}
RNA family model construction | | | | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=8f2d958cee428ca1){:target="_blank"} | |
Scan for C/D-box sequences with segmentation-fold | | | | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=3b717623054d5125){:target="_blank"} | |
Small Non-coding RNA Clustering using BlockClust | | [<i class="fa fa-laptop" aria-hidden="true"></i>](https://galaxyproject.github.io/training-material/topics/transcriptomics/tutorials/small_ncrna_clustering/tutorial.html){:target="_blank"} | [<i class="fa fa-files-o" aria-hidden="true"></i>](https://zenodo.org/record/1491876){:target="_blank"} | [<i class="fa fa-share-alt" aria-hidden="true"></i>]({{ page.website }}/workflows/run?id=c7026cd5578c8678){:target="_blank"} | | [<i class="fa fa-list-ul" aria-hidden="true"></i>]({{ page.website }}/u/videmp/h/rna-workbench-small-non-coding-rna-clustering-using-blockclust){:target="_blank"}
Expand All @@ -56,9 +56,9 @@ In this section we list all tools that have been integrated in the RNA workbench
Tool | Description | Reference
--- | --- | ---
[antaRNA]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fantarna%2Fantarna){:target="_top"} | Possibility of inverse RNA structure folding and a specification of a GC value constraint | [Kleinkauf et al. 2015](https://doi.org/10.1093/bioinformatics/btv319){:target="_blank"}
CoFold | A thermodynamics-based RNA secondary structure folding algorithm | [Proctor and Meyer, 2015](https://doi.org/10.1093/nar/gkt174){:target="_blank"}
[CoFold]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fcofold%2Fcofold){:target="_top"} | A thermodynamics-based RNA secondary structure folding algorithm | [Proctor and Meyer, 2015](https://doi.org/10.1093/nar/gkt174){:target="_blank"}
[Kinwalker]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fkinwalker%2Frbc_kinwalker){:target="_top"} | Algorithm for cotranscriptional folding of RNAs to obtain the min. free energy structure | [Geis et al. 2008](https://doi.org/10.1016/j.jmb.2008.02.064){:target="_blank"}
MEA | Prediction of maximum expected accuracy RNA secondary structures | [Amman et al. 2013](https://doi.org/10.1007/978-3-319-02624-4_1){:target="_blank"}
[MEA]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fmea%2Fmea){:target="_top"} | Prediction of maximum expected accuracy RNA secondary structures | [Amman et al. 2013](https://doi.org/10.1007/978-3-319-02624-4_1){:target="_blank"}
[RNAshapes]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Frnashapes%2FRNAshapes){:target="_top"} | Structures to a tree-like domain of shapes, retaining adjacency and nesting of structural features | [Janssen and Giergerich, 2014](https://doi.org/10.1093/bioinformatics/btu649){:target="_blank"}
[RNAz]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Frnaz%2Frnaz){:target="_top"} | Predicts structurally conserved and therm. stable RNA secondary structures in mult. seq. alignments | [Washietl et al. 2005](https://doi.org/10.1073/pnas.0409169102){:target="_blank"}
[segmentation-fold]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fyhoogstrate%2Fsegmentation_fold%2Fsegmentation_fold){:target="_top"}| An application that predicts RNA 2D-structure with an extended version of the Zuker algorithm | -
Expand All @@ -83,7 +83,7 @@ Tool | Description | Reference
[ARAGORN]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrna_prediction%2Faragorn_trna){:target="_top"} | A tool to identify tRNA and tmRNA genes | [Laslett and Canback, 2004](https://doi.org/10.1093/nar/gkh152){:target="_blank"}
[Fusion Matcher (FuMa)]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fyhoogstrate%2Ffuma%2Ffuma){:target="_top"} | A tool that reports identical fusion genes based on gene-name annotations | [Hoogstrate et al. 2016](https://doi.org/10.1093/bioinformatics/btv721){:target="_blank"}
[GotohScan]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fgotohscan%2Frbc_gotohscan){:target="_top"} | A search tool that finds shorter sequences in large database sequences | [Hertel et al. 2009](https://doi.org/10.1093/nar/gkn1084){:target="_blank"}
INFERNAL | A tool searching DNA sequence databases for RNA structure and sequence similarities | [Nawrocki et al. 2015](https://doi.org/10.1093/nar/gku1063){:target="_blank"}
[INFERNAL]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Finfernal%2Finfernal_cmsearch){:target="_top"} | A tool searching DNA sequence databases for RNA structure and sequence similarities | [Nawrocki et al. 2015](https://doi.org/10.1093/nar/gku1063){:target="_blank"}
[RNABOB]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Frnabob%2Frbc_rnabob){:target="_top"} | A tool for fast pattern searching for RNA secondary structures | -
[RNAcode]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Frnacode%2Frbc_rnacode){:target="_top"} | Predicts protein coding regions in a a set of homologous nucleotide sequences | [Washietl et al. 2011](https://doi.org/10.1261/rna.2536111){:target="_blank"}
[tRNAscan]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fbgruening%2Ftrna_prediction%2Ftrnascan){:target="_top"} | Searches for tRNA genes in genomic sequences | [Lowe and Eddy, 1997](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC146525/){:target="_blank"}
Expand All @@ -94,7 +94,7 @@ INFERNAL | A tool searching DNA sequence databases for RNA structure and sequenc

Tool | Description | Reference
--- | --- | ---
AREsite2 | A database for AU-/GU-/U-rich elements in human and model organisms | [Fallmann et al. 2016](https://doi.org/10.1093/nar/gkv1238){:target="_blank"}
[AREsite2]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Faresite2%2FAREsite2_REST){:target="_top"} | A database for AU-/GU-/U-rich elements in human and model organisms | [Fallmann et al. 2016](https://doi.org/10.1093/nar/gkv1238){:target="_blank"}
[DoRiNA]({{ page.website }}/tool_runner/data_source_redirect?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fdorina%2Fdorina_search){:target="_top"} | A database of RNA interactions in post-transcriptional regulation | [Blin et al. 2014](https://doi.org/10.1093/nar/gku1180){:target="_blank"}
[PARalyzer]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fparalyzer%2Fparalyzer){:target="_top"}| An algorithm to generate a map of interacting RNA-binding proteins and their targets | [Corcoran et al. 2011](https://doi.org/10.1186/gb-2011-12-8-r79){:target="_blank"}
[Piranha]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Fpiranha%2Fpiranha){:target="_top"} | A peak-caller for CLIP- and RIP-seq data | -
Expand All @@ -104,7 +104,7 @@ AREsite2 | A database for AU-/GU-/U-rich elements in human and model organisms |

Tool | Description | Reference
--- | --- | ---
TargetFinder | A tool to predict small RNA binding sites on target transcripts from a sequence database | -
[TargetFinder]({{ page.website }}/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Frnateam%2Ftargetfinder%2Ftargetfinder) | A tool to predict small RNA binding sites on target transcripts from a sequence database | -
{: .table.table-striped .tooltable}

## RNA Seq and HTS analysis
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