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MonashProteomics
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FragPipe-Analyst
GNU General Public License v3.0
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k-means clustering were not performed if no imputation used
#47
hsiaoyi0504
closed
1 year ago
1
Redundant column names in TMT combined_annotation.txt file
#46
ginnyintifa
closed
1 year ago
9
PCA plot other than PC1 and PC2
#45
hsiaoyi0504
closed
1 year ago
0
Parameters are hard-coded in reports
#44
hsiaoyi0504
closed
1 year ago
1
PCA should show sample name/ID rather than condition
#43
hsiaoyi0504
closed
1 year ago
1
Only features with low enough percentage of missing values should be imputed
#42
hsiaoyi0504
closed
1 year ago
1
Handle errors when generating report
#41
hsiaoyi0504
closed
1 year ago
0
Report couldn't be downloaded for the Aspirin dataset
#40
hsiaoyi0504
closed
1 year ago
2
PCA plot now can be colored by plex number in TMT
#39
hsiaoyi0504
closed
1 year ago
0
Add a version number to somewhere in the webpage so that we can track the versions.
#38
fcyu
closed
1 year ago
1
Change all `Fragpipe` to `FragPipe`
#37
fcyu
closed
1 year ago
2
Filtering based on samples in same condition
#36
hsiaoyi0504
closed
1 year ago
3
An option to choose intensity or MaxLFQ intensity for LFQ
#35
hsiaoyi0504
closed
1 year ago
2
missing value heatmap should use the raw data rather than a filtered version of data
#34
hsiaoyi0504
closed
1 year ago
3
More flexible control of enrichment visualization
#33
hsiaoyi0504
closed
1 year ago
1
DIA example needs to be adjusted
#32
hsiaoyi0504
closed
1 year ago
3
No imputation as default
#31
hsiaoyi0504
closed
1 year ago
0
check more than one condition exist before processed
#30
hsiaoyi0504
closed
1 year ago
1
color PCA by plex number in TMT
#29
hsiaoyi0504
closed
1 year ago
0
Phospho-Kinase enrichment analysis through KEA3
#28
hsiaoyi0504
closed
1 year ago
2
Added parallel config file and fixed download report error in Dockerfile
#27
Hailey-Z
closed
1 year ago
0
The scrollbar of result table is not obvious and hard to use
#26
hsiaoyi0504
closed
1 year ago
1
Keep subset of imputation methods available
#25
hsiaoyi0504
closed
1 year ago
1
Different report should be used for different experimental type
#24
hsiaoyi0504
closed
1 year ago
1
Enrichment analysis doesn't separate up and down regulated parts
#23
hsiaoyi0504
closed
1 year ago
2
modified Dockerfile and footer
#22
Hailey-Z
closed
1 year ago
0
User submits the annotation.txt (rather than combined_annotation.txt) and it will crash the app.
#21
hsiaoyi0504
closed
1 year ago
0
Update column names used for DIA
#20
hsiaoyi0504
closed
1 year ago
2
Gene set used for enrichment analysis
#19
hsiaoyi0504
closed
1 year ago
1
Which enrichment tool used
#18
hsiaoyi0504
closed
1 year ago
1
Add a loading visualization/animation to let user feel safe to wait longer
#17
hsiaoyi0504
closed
1 year ago
1
Missing of linked example dataset
#16
Hailey-Z
closed
1 year ago
1
Absence/Presence error on DIA analysis
#15
Hailey-Z
closed
1 year ago
7
Individual plots section not work on DIA analysis
#14
Hailey-Z
closed
1 year ago
0
Dotplot for enrichment result
#13
hsiaoyi0504
closed
1 year ago
2
fix a bug that the select input for comparisons in pathway enrichment doesn't work
#12
hsiaoyi0504
closed
1 year ago
0
The pathway enrichment analysis is visualized in different way compared with GO enrichment
#11
hsiaoyi0504
closed
1 year ago
1
FDRtools might fail
#10
hsiaoyi0504
closed
1 year ago
0
Download internal SummarizedExperiment .RData object
#9
hsiaoyi0504
closed
1 year ago
1
add a check for TMT annotation file
#8
hsiaoyi0504
closed
1 year ago
0
Avoid updating analysis without pressing the submit button again
#7
hsiaoyi0504
closed
1 year ago
3
No imputation option or shows number/percentage of imputed values in each condition
#6
hsiaoyi0504
closed
1 year ago
1
use impute_customized for TMT and enhance error handling for enrichment analysis
#5
hsiaoyi0504
closed
1 year ago
1
MA plot
#4
hsiaoyi0504
closed
1 year ago
1
make tmt exp desgin file more flexible
#3
hsiaoyi0504
closed
1 year ago
0
Test Fragpipe output with combined_annotation.txt
#2
hsiaoyi0504
closed
1 year ago
4
add interactive PCA
#1
hsiaoyi0504
closed
1 year ago
0
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