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New and updated tools 2024-11-06 #328

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39 changes: 39 additions & 0 deletions _posts/2024-11-06-tool-updates.md
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Original file line number Diff line number Diff line change
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---
site: freiburg
title: 'Galaxy Australia tool updates 2024-11-06'
tags: [tools]
supporters:
- galaxyaustralia
- melbinfo
- qcif
---


<style>
table {
width: 100%;
margin: 10px 20px;
}
table th {
display: none;
}
td {
padding: 3px 5px;
}
tr td:nth-child(1) {
vertical-align: top;
width: 25%;
}
</style>

### Tools updated

| Section | Tool |
|---------|-----|
| **Convert Formats** | agat [d6ede73082da](https://toolshed.g2.bx.psu.edu/view/bgruening/agat/d6ede73082da)<br/>ucsc_wigtobigwig [fa49730d1d4b](https://toolshed.g2.bx.psu.edu/view/iuc/ucsc_wigtobigwig/fa49730d1d4b) |
| **HiCExplorer** | hicexplorer_hicbuildmatrix [0f611e7d7858](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicbuildmatrix/0f611e7d7858)<br/>hicexplorer_hicmergematrixbins [f72063d9426b](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergematrixbins/f72063d9426b)<br/>hicexplorer_hicpca [1da5f169b491](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicpca/1da5f169b491)<br/>hicexplorer_hicplotmatrix [f741330d4a71](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotmatrix/f741330d4a71) |
| **Metabolomics** | isolib [2b1118bce0b1](https://toolshed.g2.bx.psu.edu/view/recetox/isolib/2b1118bce0b1)<br/>recetox_aplcms_align_features [ec196e27a61a](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_align_features/ec196e27a61a)<br/>recetox_aplcms_compute_clusters [59c393d35e0e](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_clusters/59c393d35e0e)<br/>recetox_aplcms_compute_template [50b9918aeff2](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_compute_template/50b9918aeff2)<br/>recetox_aplcms_correct_time [a82db010c53e](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_correct_time/a82db010c53e)<br/>recetox_aplcms_generate_feature_table [89178a72388a](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_generate_feature_table/89178a72388a)<br/>recetox_aplcms_merge_known_table [b7c8a44b9cc1](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_merge_known_table/b7c8a44b9cc1)<br/>recetox_aplcms_recover_weaker_signals [f92b1b64da93](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_recover_weaker_signals/f92b1b64da93)<br/>recetox_aplcms_remove_noise [7acd11ddc061](https://toolshed.g2.bx.psu.edu/view/recetox/recetox_aplcms_remove_noise/7acd11ddc061) |
| **Nanopore** | dorado [c2a23340f233](https://toolshed.g2.bx.psu.edu/view/galaxy-australia/dorado/c2a23340f233)<br/>dorado_pod5_convert [3479b06460a4](https://toolshed.g2.bx.psu.edu/view/galaxy-australia/dorado_pod5_convert/3479b06460a4) |
| **RNA-seq** | featurecounts [1b851f87fbe0](https://toolshed.g2.bx.psu.edu/view/iuc/featurecounts/1b851f87fbe0) |
| **Single-cell** | hicexplorer_chicaggregatestatistic [952abbc4b1de](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicaggregatestatistic/952abbc4b1de)<br/>hicexplorer_chicdifferentialtest [f1c35f3f310d](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicdifferentialtest/f1c35f3f310d)<br/>hicexplorer_chicexportdata [cab616fe7e64](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicexportdata/cab616fe7e64)<br/>hicexplorer_chicplotviewpoint [b9ab56aecd18](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicplotviewpoint/b9ab56aecd18)<br/>hicexplorer_chicqualitycontrol [9ea228a9afc8](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicqualitycontrol/9ea228a9afc8)<br/>hicexplorer_chicsignificantinteractions [f8320df1866b](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicsignificantinteractions/f8320df1866b)<br/>hicexplorer_chicviewpointbackgroundmodel [c354255ff705](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpointbackgroundmodel/c354255ff705)<br/>hicexplorer_chicviewpoint [c4ed35f4f77f](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_chicviewpoint/c4ed35f4f77f)<br/>hicexplorer_hicadjustmatrix [782bdcb775fb](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicadjustmatrix/782bdcb775fb)<br/>hicexplorer_hicaggregatecontacts [63c8377c58b3](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaggregatecontacts/63c8377c58b3)<br/>hicexplorer_hicaverageregions [fe3aa71590d5](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicaverageregions/fe3aa71590d5)<br/>hicexplorer_hiccomparematrices [4f9305d3bb34](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccomparematrices/4f9305d3bb34)<br/>hicexplorer_hiccompartmentspolarization [a315574104c6](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccompartmentspolarization/a315574104c6)<br/>hicexplorer_hicconvertformat [a83732c79949](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicconvertformat/a83732c79949)<br/>hicexplorer_hiccorrectmatrix [30d7390bc918](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrectmatrix/30d7390bc918)<br/>hicexplorer_hiccorrelate [cd40ca76865a](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hiccorrelate/cd40ca76865a)<br/>hicexplorer_hicdetectloops [bf9379529c3e](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdetectloops/bf9379529c3e)<br/>hicexplorer_hicdifferentialtad [07dd436ea686](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicdifferentialtad/07dd436ea686)<br/>hicexplorer_hicfindrestrictionsites [f1b3902f8baf](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicfindrestrictionsites/f1b3902f8baf)<br/>hicexplorer_hichyperoptdetectloops [bb8849fca57c](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hichyperoptdetectloops/bb8849fca57c)<br/>hicexplorer_hicinfo [b0f33533181d](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinfo/b0f33533181d)<br/>hicexplorer_hicinterintratad [32173084d53f](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicinterintratad/32173084d53f)<br/>hicexplorer_hicmergedomains [4b194e675916](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergedomains/4b194e675916)<br/>hicexplorer_hicmergeloops [910c6a1c3a27](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicmergeloops/910c6a1c3a27)<br/>hicexplorer_hicnormalize [2aa5b6b65197](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicnormalize/2aa5b6b65197)<br/>hicexplorer_hicplotaverageregions [9b383d429659](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotaverageregions/9b383d429659)<br/>hicexplorer_hicplotdistvscounts [06ced663d24f](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotdistvscounts/06ced663d24f)<br/>hicexplorer_hicplotsvl [beb5b5917d2f](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicplotsvl/beb5b5917d2f)<br/>hicexplorer_hicquickqc [5cbd7a902a8d](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicquickqc/5cbd7a902a8d)<br/>hicexplorer_hicsummatrices [f81750434d70](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicsummatrices/f81750434d70)<br/>hicexplorer_hictransform [1de2276f633f](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hictransform/1de2276f633f)<br/>hicexplorer_hicvalidatelocations [cef9fb4ece1c](https://toolshed.g2.bx.psu.edu/view/bgruening/hicexplorer_hicvalidatelocations/cef9fb4ece1c)<br/>raceid_clustering [49776718ae90](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_clustering/49776718ae90)<br/>raceid_filtnormconf [8b917923f7d4](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_filtnormconf/8b917923f7d4)<br/>raceid_inspectclusters [c7ddb719554d](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspectclusters/c7ddb719554d)<br/>raceid_inspecttrajectory [6e90c8adf84f](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_inspecttrajectory/6e90c8adf84f)<br/>raceid_trajectory [2bfd55b87af3](https://toolshed.g2.bx.psu.edu/view/iuc/raceid_trajectory/2bfd55b87af3)<br/>sceasy_convert [5c9b16bdbd5e](https://toolshed.g2.bx.psu.edu/view/iuc/sceasy_convert/5c9b16bdbd5e)<br/>sinto_barcode [fb61eb03e313](https://toolshed.g2.bx.psu.edu/view/iuc/sinto_barcode/fb61eb03e313)<br/>sinto_fragments [6f66f523a9b7](https://toolshed.g2.bx.psu.edu/view/iuc/sinto_fragments/6f66f523a9b7) |
| **Variant Calling** | cutesv [cb441f258c37](https://toolshed.g2.bx.psu.edu/view/iuc/cutesv/cb441f258c37) |