You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
<h4class="my-3">What do you think of the {{ lab_name }}?</h4>
32
+
<button
33
+
class="ga-btn"
34
+
data-bs-toggle="modal"
35
+
data-bs-target="#feedbackModal"
36
+
>
37
+
Give feedback
38
+
</button>
39
+
</section>
40
+
{% endif %}
41
+
42
+
<sectionclass="my-5">
43
+
<h4class="mb-3">Cite Us</h4>
44
+
</section>
45
+
46
+
<sectionclass="my-5">
47
+
If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using this webpage.
48
+
<!-- If you find the {{ lab_name }} Lab and the effort of the {{ lab_name }} community useful for your research, please cite us using our <a href="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>-->
Welcome to the Galaxy {{ site_name }} {{ lab_name }} by the {{ lab_name }} community!
4
+
</p>
5
+
6
+
<p>
7
+
#Here include an intro to your page, see the ex mple below from the microgalaxy community
8
+
# Whether you're working with microbiome samples or bacterial isolates, long or short reads, shotgun or 16S sequencing, genomics, transcriptomics, proteomics, metabolomics, or integrative multi-omics analysis—this is the place for you! Learn more about the Microbiology Lab and the effort of the microGalaxy community in our <ahref="https://www.biorxiv.org/content/10.1101/2024.12.23.629682v1" target="_blank" rel="noopener noreferrer">preprint</a>. </p>
9
+
<p>
10
+
<a
11
+
href="#"
12
+
data-bs-toggle="modal"
13
+
data-bs-target="#infoModal">
14
+
How does this page relate to Galaxy {{ site_name }}?
This site <em>{{ subdomain }}.{{ root_domain }}</em> is connected to the same server as <em>{{ root_domain }}</em>, but with an interface dedicated to helping our {{ analysis_name }} researchers. Your history, jobs and data quota are shared with the "Base" Galaxy {{ site_name }} website.
30
+
</p>
31
+
<p><aclass="ga-btn" href="https://{{ root_domain }}" target="_blank">Take me back to Galaxy {{ site_name }}</a></p>
32
+
<p><aclass="ga-btn" href="https://{{ root_domain }}/about">What is Galaxy {{ site_name }}?</a></p>
# - title_md: <code>Pavian</code> - Interactive analysis of metagenomics data
54
+
# description_md: >
55
+
# An interactive browser application for analyzing and visualization metagenomics classification results from classifiers such as Kraken, KrakenUniq, Kraken 2, Centrifuge and MetaPhlAn. Pavian also provides an alignment viewer for validation of matches to a particular genome.
# Connected tutorials to train you to perform microbial data analysis.
66
+
# content:
67
+
# - title_md: Introduction to Galaxy and Sequence analysis
68
+
# description_md: >
69
+
# New to Galaxy and/or the field of genomics? In this learning pathway, you will learn how to use Galaxy for analysis, and will be guided through the most common first steps of any genome analysis; quality control and a mapping or assembly of your genomic sequences.
Any user of Galaxy {{ site_name }} can request support online!
20
+
button_md: Request support
21
+
button_link: "{{ support_url }}"
22
+
button_icon: help
23
+
button_tip: Request support
24
+
# - title_md: microGalaxy chat room
25
+
# description_md: >
26
+
# Chat with members of the microGalaxy community on Matrix
27
+
# button_link: "{{ microgalaxy_matrix }}"
28
+
# button_md: Matrix channel
29
+
# button_icon: social
30
+
# button_tip: Join the chat
31
+
32
+
- id: faq
33
+
title: FAQ
34
+
content:
35
+
- title_md: How can I increase my storage quota?
36
+
description_md: >
37
+
Please submit a quota request if your Galaxy account reaches its data storage limit. Requests are usually provisioned quickly if you provide a reasonable use case for your request.
38
+
button_md: Request
39
+
button_link: "{{ quota_request_url }}"
40
+
button_tip: Request quota
41
+
button_icon: help
42
+
- title_md: Can I upload sensitive data?
43
+
description_md: >
44
+
No, please do not upload personal or sensitive, such as human health or clinical data. Please see our
45
+
[Privacy Policy]({{ data_policy_url }})
46
+
page for definitions of sensitive and health-related information.
47
+
48
+
Please also make sure you have read our
49
+
[Terms of Service]({{ terms_url }}),
50
+
which covers hosting and analysis of research data.
51
+
- title_md: Is my data private?
52
+
description_md: >
53
+
Please read our
54
+
[Privacy Policy]({{ data_policy_url }})
55
+
for information on your personal data and any data that you upload.
This Galaxy space is the result of hard, collaborative work by many contributors.
10
+
# It is maintained by the microGalaxy Community of Practice.
11
+
# This group unites scientists like yourself with software developers and bioinformaticians to create, share, and test resources to make microvial data analysis easier.
12
+
# Check out our site and join our community via [microGalaxy mailing list](https://lists.galaxyproject.org/lists/microgalaxy@lists.galaxyproject.org)!
13
+
# - title_md: Chat with others!
14
+
# description_md: >
15
+
# Use our matrix channel to chat with others from microGalaxy community
16
+
# button_link: "{{ microgalaxy_matrix }}"
17
+
# button_md:
18
+
# button_tip: Visit microGalaxy
19
+
# button_icon: social
20
+
21
+
- id: governance
22
+
title: How is the Galaxy Community organised?
23
+
heading_md: >
24
+
Learn about the
25
+
{gtn modal}[governance structure of Galaxy communities](https://training.galaxyproject.org/training-material/topics/community/faqs/governance_structure.html) on the GTN.
26
+
content: []
27
+
28
+
- id: links
29
+
title: Galaxy Community support links
30
+
content:
31
+
- title_md: "For general Galaxy support"
32
+
description_md: "General Galaxy support"
33
+
button_link: "{{ general_support }}"
34
+
button_tip: Galaxy Support
35
+
button_icon: help
36
+
- title_md: "General Help Forum"
37
+
description_md: "Access general Galaxy help"
38
+
button_link: "{{ galaxy_help_url }}"
39
+
button_tip: Help forum
40
+
button_icon: help
41
+
- title_md: "Galaxy Training Network Slack Workspace"
42
+
description_md: "Join the GTN Slack community"
43
+
button_link: "{{ gtn_slack_url }}"
44
+
button_tip: Slack channel - Join the GTN Slack community.
45
+
button_icon: social
46
+
- title_md: "Galaxy Training Network Community Chat Room"
47
+
description_md: "Connect on the GTN Matrix chat"
48
+
button_link: "{{ gtn_matrix_channel }}"
49
+
button_tip: Matrix channel - Connect on the GTN Matrix chat.
50
+
button_icon: social
51
+
# - title_md: "microGalaxy User Community Chat Room"
52
+
# description_md: "Join the microGalaxy Matrix chat"
53
+
# button_link: "{{ microgalaxy_matrix }}"
54
+
# button_tip: Matrix channel - Join the microGalaxy Matrix chat.
55
+
# button_icon: social
56
+
- title_md: "General Galaxy Project Chat Room"
57
+
description_md: "Join the Galaxy project chat"
58
+
button_link: "{{ galaxy_matrix_channel }}"
59
+
button_tip: Matrix channel - Join the Galaxy project chat.
Copy file name to clipboardExpand all lines: communities/proteomics/metadata/tool_status.tsv
+2-12Lines changed: 2 additions & 12 deletions
Original file line number
Diff line number
Diff line change
@@ -1,16 +1,12 @@
1
1
Suite IDSuite ownerDescriptionTo keepDeprecated
2
2
MALDIquant galaxyp MALDIquant provides a complete analysis pipeline for MALDI-TOF and other 2D mass spectrometry data. False False
3
-
b2btools iuc This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work.
4
3
bed_to_protein_map galaxyp Converts a BED file to a tabular list of exon locations False False
5
4
bioconductor-msnbase recetox MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data. False False
6
5
bioconductor_mzr recetox Galaxy wrapper for the Bioconductor mzR package, enabling conversion between common mass spectrometry data formats (mzML, mzXML, netCDF) within Galaxy workflows.
7
6
bioconductor_scp recetox scp is a package for the single cell proteomics data processing. False False
8
7
bumbershoot galaxyp
9
8
calisp galaxyp Calgary approach to isotopes in proteomics False False
10
9
cardinal galaxyp Statistical and computational tools for analyzing mass spectrometry imaging datasets
11
-
cite_seq_count iuc Count CMO/HTO False False
12
-
colabfold iuc Protein prediction based on AlphaFold2 False False
13
-
constava iuc Calculate 'conformational states probabilities' and 'conformational state variability' from a protein structure ensemble
data_manager_eggnog_mapper galaxyp downloads eggnog data for eggnog-mapper False False
@@ -48,12 +44,11 @@ msms_extractor galaxyp Extract MS/MS scans from the mzML file(s) based on PSM re
48
44
msstatstmt galaxyp MSstats tool for analyzing mass spectrometry proteomic datasets False False
49
45
msstatstmt galaxyp MSstatsTMT protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling False False
50
46
mt2mq galaxyp Tool to prepare metatranscriptomic outputs from ASaiM for Metaquantome False False
51
-
multigsea iuc GSEA-based pathway enrichment analysis for multi-omics data False False
52
47
mz_to_sqlite galaxyp Creates a SQLite database for proteomics data False False
53
48
mzml_validator recetox mzML Validator checks if mzML file validates against XML Schema Definition of HUPO Proteomics Standard Initiative.
54
49
mzspeclib recetox mzspeclib is a library and set of tools for handling, converting, and validating mass spectral libraries in a standardized format. This suite provides Galaxy wrappers for mzspeclib's core functionalities, including conversion and validation of spectral libraries.
55
-
openms bgruening OpenMS in version 2.1.
56
50
openms galaxyp OpenMS Suite for LC/MS data management and analyses False False
51
+
openms bgruening OpenMS in version 2.1.
57
52
pep_pointer galaxyp PepPointer categorizes peptides by their genomic coordinates. False False
58
53
pepquery galaxyp A peptide-centric MS search engine for novel peptide identification and validation. False False
59
54
pepquery2 galaxyp PepQuery2 peptide-centric MS search for peptide identification and validation False False
@@ -63,9 +58,8 @@ peptimapper genouest Proteogenomics workflow for the expert annotation of eukary
63
58
pepxml_to_xls galaxyp Convert PepXML to Tabular False False
64
59
percolator galaxyp Percolator False False
65
60
pmd_fdr galaxyp Calculate Precursor Mass Discrepancy (PMD) for MS/MS False False
66
-
prot_scriber iuc Protein annotation of short human readable descriptions False False
67
61
protease_prediction bgruening This tool can learn the cleavage specificity of a given class of proteases.
68
-
proteinortho iuc Proteinortho is a tool to detect orthologous proteins/genes within different species. False False
62
+
protein_mosaic_q galaxyp Calculate the Mosaic Q descriptor and visualise amino acid clustering in protein structures
69
63
proteomics_improviser bgruening Visualisation of PepXML files
70
64
proteomics_moff galaxyp moFF (a modest Feature Finder) extracts MS1 intensities from RAW and mzML spectrum files. False False
71
65
proteomiqon_joinquantpepionswithproteins galaxyp The tool JoinQuantPepIonsWithProteins combines results from ProteinInference and PSMBasedQuantification. False False
@@ -87,14 +81,10 @@ pyteomics galaxyp Tools using the pyteomics library False False
87
81
quantp galaxyp Correlation between protein and transcript abundance False False
88
82
quantwiz_iq galaxyp Isobaric Quantitation using QuantWiz-IQ False False
![github-actions[bot]](https://avatars.githubusercontent.com/in/15368?v=4&size=40){kind=avatar}
0 commit comments