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galaxyproject / tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission
https://galaxyproject.org/iuc
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Tools that may get worked on #1657

Open mblue9 opened 6 years ago

mblue9 commented 6 years ago

Hello all,

Just wanted to let people know what tools I'm working on (or might work on in the future), in case anyone else is interested in these. I'm concentrating on RNA-seq/ChIP-seq/ATAC-seq workflows at the moment and will get onto these things as I can get the time.

bcGST for Gene Set Testing (for targeted assays, Nanostring, proteomics) https://www.biorxiv.org/content/early/2017/12/28/240234.full.pdf+html

Glimma for interactive visualisation of gene expression data

CNVkit for CNVs from targeted sequencing

I've made a start on some other wrappers too:

and some more distant Future plans are to try to add in these tools below (I may have missed some and they are in no particular order, and I may decide to do some from below before above. I'll work on them based on what we need at my institute):

ascend for Single Cell https://www.biorxiv.org/content/early/2017/10/23/207704 diffHic for HiC https://bioconductor.org/packages/release/bioc/html/diffHic.html limma::diffSplice and edgeR::diffSpliceDGE for Alternative Splicing csaw for ChIP-seq https://bioconductor.org/packages/release/bioc/html/csaw.html Subread/Rsubread for Mapping https://bioconductor.org/packages/release/bioc/html/Rsubread.html (featureCounts is from the Subread package) More of limma (e.g. more complicated designs like interactions) http://bioconductor.org/packages/release/bioc/html/limma.html missMethyl for Methylation arrays https://bioconductor.org/packages/release/bioc/html/missMethyl.html Survival analysis tool something like https://github.com/crukci-bioinformatics/galaxy-survival Cancer Genomics Tools https://academic.oup.com/gigascience/article/6/5/1/3064403 Canary for Clinical Amplicon sequencing https://github.com/PapenfussLab/Canary GRIDSS for Genomic Rearrangements https://github.com/PapenfussLab/gridss Clove for Structural Variant classification https://github.com/PapenfussLab/clove HYSYS for QC (sample swaps) https://github.com/PapenfussLab/HaveYouSwappedYourSamples Clinker for Visualising Fusions https://github.com/Oshlack/Clinker/wiki STRetch for STR expansions https://github.com/Oshlack/STRetch Splatter for Simulation of scRNA-seq data (to help assess analysis methods as there are many https://www.scrna-tools.org/. I was thinking this tool could be useful/fun for creating training data e.g. to teach how scRNA-seq analyses/tools compare, how things like batch effects, outliers can affect results etc) https://bioconductor.org/packages/release/bioc/html/splatter.html

I obviously may not get the time to work on them all but this is the current wishlist.

mvdbeek commented 6 years ago

That looks like a great list! I have successfully used https://cran.r-project.org/web/packages/VennDiagram/index.html for some one-off plotting, the advantage is that the package can draw the sizes to scale and deal with multiple datastes (5 is the max, I think) ... even if in this case one should probably resort to bar charts or some other plotting (https://github.com/hms-dbmi/UpSetR ?).

mblue9 commented 6 years ago

Thanks @mvdbeek that's good to know! I had started on updating this Venn diagram tool from the toolshed https://github.com/peterjc/pico_galaxy/tree/master/tools/venn_list but I'll take a look at that one too. As a Venn diagram tool would be useful for lots of things I think so it would be good to have an IUC-one. Although I don't know yet when I'll find the time to get back onto Venns.

mblue9 commented 5 years ago

Some priorities have changed (in relation to these tools) since I wrote this so I've changed this to a "might get worked on" and removed the tools that @mvdbeek has added (RUVseq and UpSetR), thanks for adding those!

mvdbeek commented 5 years ago

I do have to do some volcano plots and ma-plots using labels and group highlights -- I might look into that very soon if you haven't already.

bebatut commented 5 years ago

@mvdbeek did you add UpSetR?

mvdbeek commented 5 years ago

Yes, as wrapped in intervene -- https://github.com/galaxyproject/tools-iuc/pull/2074

bebatut commented 5 years ago

I totally missed it. Thanks for that!

mblue9 commented 5 years ago

Cool @mvdbeek, I have only made a rough start on the volcano plot but if you want a look I've put it here https://github.com/galaxyproject/tools-iuc/pull/2114

jdavcs commented 3 years ago

I'll take on the CVNkit wrapper, unless anyone is working on it.