Owner

lgatto

6 indexed repositories · View on GitHub

MSnbase
Base Classes and Functions for Mass Spectrometry and Proteomics

R · 137 stars
pRoloc
A unifying bioinformatics framework for organelle proteomics

R · 16 stars
pRolocGUI
Interactive visualisation and exploration of spatial proteomics data

R · 8 stars
rpx
R Interface to the ProteomeXchange Repository

R · 7 stars
pRolocdata
Data accompanying the pRoloc package

R · 6 stars
mulink-qfeatures

R · 1 star

Beginner friendly Everything

Open All

Differences before and after write/read Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

lgatto/mulink-qfeatures#6 · Opened Sep 4, 2026
brunner2022: some dimnames are changed Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

lgatto/mulink-qfeatures#5 · Opened Sep 4, 2026
Empty Assays Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

lgatto/mulink-qfeatures#3 · Opened Sep 4, 2026
Comparing ai2025 before after h5mu export Open

Difficulty 3/5 1-2 days Newbie friendliness 64/100

lgatto/mulink-qfeatures#2 · 4 comments · Opened Sep 4, 2026
plot(itraqdata2[[i]], s, main = s) issues warning Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

lgatto/MSnbase#613 · 2 comments · Opened Apr 8, 2026
filterFile gives "object of type 'S4' is not subsettable" error Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/MSnbase#611 · 1 comment · Opened Aug 14, 2025
Problem creating PXD object on the cluster Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/rpx#30 · Opened Jun 6, 2025
Unable to use higher iterations and burnin for tagmMcmcTrain Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lgatto/pRoloc#158 · 13 comments · Opened Apr 21, 2025
compatibility with matrix of markers Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lgatto/pRolocGUI#120 · Opened Mar 14, 2025
Deprecation of functions Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lgatto/pRoloc#156 · 2 comments · Opened Feb 26, 2025
Consider changing name of getMarkers() Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

lgatto/pRoloc#155 · Opened Jan 9, 2025
Update titles of datasets Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lgatto/pRolocdata#76 · Opened Dec 5, 2024
A bug in reduce function Open

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

lgatto/MSnbase#607 · 1 comment · 1 reaction · Opened Nov 15, 2024
Add data from A549 cancer LOPIT Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lgatto/pRolocdata#75 · Opened Oct 4, 2024
Modification of plot2D to allow filled characters Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

lgatto/pRoloc#152 · 4 comments · Opened Oct 4, 2024
Moved content of inst/extdata to the pRolocdata dataverse Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/pRolocdata#74 · 2 comments · Opened Sep 17, 2024
MSnSet <-> SummarizedExperiment Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

lgatto/pRoloc#150 · 1 reaction · Opened Sep 5, 2024
invalid class “MIAPE” object: invalid object for slot "instrumentModel" in class "MIAPE": got class "list", should be or extend class "character" from Autotuner Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/MSnbase#603 · 6 comments · Opened Jun 13, 2024
Using PXD015169 data from PRIDE Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/rpx#23 · 2 comments · Opened Apr 3, 2023
FTP status was '550 Requested action not taken; file unavailable' Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

lgatto/rpx#21 · 14 comments · Opened Mar 2, 2023
unit tests Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

lgatto/pRolocGUI#113 · Opened Sep 30, 2022
Add Cho cell data Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

lgatto/pRolocdata#71 · Opened Aug 12, 2022
Add support for more repos Open

enhancement

lgatto/rpx#20 · 2 reactions · 1 assignee · Opened Aug 10, 2022
Add data from Valerio human keratinocytes Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

lgatto/pRolocdata#70 · Opened Apr 7, 2022
change map colours to be consistent with new shiny apps Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

lgatto/pRolocGUI#111 · Opened Jan 25, 2022
Add data from Olsen et al 2021 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lgatto/pRolocdata#69 · Opened Dec 10, 2021
Unexpected output from fDataToUnknown Open

lgatto/pRoloc#144 · 1 assignee · Opened Dec 10, 2021
New RNGseed in BiocParallel Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

lgatto/pRoloc#143 · Opened Oct 9, 2021
add CF LOPIT data Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/pRolocdata#68 · Opened Oct 6, 2021
Issue with PXD012097 Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lgatto/rpx#16 · Opened Oct 6, 2021
Issue with PXD010692 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/rpx#15 · Opened Oct 5, 2021
Issue with PXD012577 Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

lgatto/rpx#14 · Opened Oct 5, 2021
Issue with PXD012922 Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

lgatto/rpx#13 · Opened Oct 5, 2021
Issue with PXD012095 Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

lgatto/rpx#12 · Opened Oct 4, 2021
add data from Oom et al. HIV proteomics Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

lgatto/pRolocdata#67 · 1 reaction · Opened Sep 9, 2021
recalibration Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

lgatto/MSnbase#552 · 4 comments · Opened Sep 8, 2021
Add data from Valerio UVA spatial proteomics Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/pRolocdata#66 · Opened Sep 7, 2021
Issue with PXD000002 Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lgatto/rpx#11 · Opened Aug 16, 2021
Google group rss feeds down Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

lgatto/rpx#7 · Opened Aug 12, 2021
add t-SNE coords to THP data Open

lgatto/pRolocdata#65 · 1 assignee · Opened Jun 29, 2021
add MDI clustering results to lps data Open

lgatto/pRolocdata#64 · 1 assignee · Opened Jun 17, 2021
Allow passing of predefined colours when loading pRolocGUI Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

lgatto/pRolocGUI#107 · Opened Apr 20, 2021
Update vignette and videos Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

lgatto/pRolocGUI#106 · Opened Apr 15, 2021
add HIV1 infection data Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

lgatto/pRolocdata#63 · Opened Mar 16, 2021
tagmPredict compatibility with Novelty TAGM results Open

bug

lgatto/pRoloc#138 · 1 assignee · Opened Sep 11, 2020
remove redundant column in Barylyuk2020ToxoLopit Open

lgatto/pRolocdata#55 · 1 assignee · Opened May 19, 2020
New features Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

lgatto/pRolocGUI#97 · Opened Apr 28, 2020
Water loss for b-fragments? Open

Awaiting response

lgatto/MSnbase#472 · 2 comments · 1 assignee · Opened May 31, 2019
PCA plot aspect Open

lgatto/pRoloc#134 · 1 assignee · Opened May 1, 2019
Novelty Tagm ToDo Open

lgatto/pRoloc#127 · 2 assignees · Opened Dec 10, 2018

lgatto

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