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APAF-bioinformatics
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ProteomeScholaR
GNU Lesser General Public License v3.0
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bring dev-jr up to main
#58
Bucket-Chemist
closed
13 hours ago
0
deAnalysisWrapperFunction does not accept group strings beginning with a number
#57
Bucket-Chemist
opened
1 day ago
1
Potential issue with chooseBestProteinAccession
#56
Bucket-Chemist
opened
1 day ago
3
reformat workbooks to meet 80 chars per line standard
#55
Bucket-Chemist
opened
5 days ago
0
move the tmp folder and contents from scripts/proteomics to results/proteomics
#54
Bucket-Chemist
opened
1 week ago
0
main to include changes made in dev
#53
IgnatiusPang
closed
1 week ago
1
merge dev-jr and dev
#52
IgnatiusPang
closed
1 week ago
1
merge dev to main before conference
#51
IgnatiusPang
closed
1 week ago
1
merge to main branch
#50
Bucket-Chemist
closed
1 week ago
1
dev
#49
Bucket-Chemist
closed
1 week ago
0
Readme.md for how to get data
#48
Bucket-Chemist
opened
1 week ago
0
Annotation mapping at top of workflow needs bugfixing for uniprot fasta - updateProteinIDs()
#47
Bucket-Chemist
closed
1 day ago
0
Glimma fork needs to be included in the install - loadDependencies()
#46
Bucket-Chemist
opened
1 week ago
0
Glimma in report for generating volcano plots
#45
Bucket-Chemist
opened
1 week ago
0
Put all the dynamic summary text and numbers up the top in an executive summary style thingo
#44
Bucket-Chemist
opened
1 week ago
0
Design matrix as an appendix in report
#43
Bucket-Chemist
opened
1 week ago
0
APAF logo as per NATA doc in the .rmd header
#42
Bucket-Chemist
opened
1 week ago
0
Technical replicate experimental design guidelines to give to client
#41
Bucket-Chemist
opened
1 week ago
0
LFC cutoff for treat, unlog it and people put in the absolute version
#40
Bucket-Chemist
opened
1 week ago
0
Bold table headers for the top10 tables in report
#39
Bucket-Chemist
opened
1 week ago
0
Sequential numbering for the QC plotting/filtering steps - currently just as names
#38
Bucket-Chemist
closed
1 day ago
0
Add option to NOT filter by proteotypic peptide
#37
Bucket-Chemist
opened
1 week ago
2
Should not delete the original filename in design matrix, copy to column to preserve
#36
Bucket-Chemist
opened
1 week ago
0
move legend for pca plots to top row of composite plot
#35
Bucket-Chemist
opened
2 weeks ago
0
Add a label for pca plots to code factor into shapes
#34
Bucket-Chemist
opened
2 weeks ago
0
Add a warning or error output when a sample is removed at any given filtering step
#33
Bucket-Chemist
opened
2 weeks ago
0
Print out best k and num neg ctrl proteins and % param used
#32
Bucket-Chemist
opened
2 weeks ago
0
Merge pull request #30 from APAF-bioinformatics/dev-jr
#31
IgnatiusPang
closed
1 month ago
0
dev-merged
#30
Bucket-Chemist
closed
1 month ago
0
Logic correction for reading fasta files to detect uniprot/non-uniprot source
#29
Bucket-Chemist
closed
2 weeks ago
0
Function to read and output the config.ini as a method section
#28
Bucket-Chemist
opened
1 month ago
0
cytoscape integration
#27
Bucket-Chemist
opened
2 months ago
0
Object-wrap RUVIII vanilla codes for compatibility with TMT with no missing values (for CMRI)
#26
IgnatiusPang
opened
2 months ago
0
Add debug or print messages for users to see that something is happening as the operation takes a while - at end of every fetch?
#25
Bucket-Chemist
closed
2 weeks ago
0
Move Uniprot annotation function into ProteomescholaR
#24
Bucket-Chemist
closed
2 weeks ago
0
Move gprofiler2 gost+gostplot call into proteomescholaR
#23
Bucket-Chemist
opened
2 months ago
0
Move clusterprofiler function to proteomescholar
#22
Bucket-Chemist
opened
2 months ago
0
Functionalise volcano plot generation for easy call on rmd
#21
Bucket-Chemist
opened
2 months ago
0
Automatically choose bar graph or heat maps for enriched pathways, turn on or off hierarchical clustering (bug avoidance switch)?
#20
IgnatiusPang
opened
2 months ago
0
Add more annotations columns in Interactive Volcano plot
#19
IgnatiusPang
opened
2 months ago
0
Functionalise generation of html report volcano plots
#18
Bucket-Chemist
opened
2 months ago
0
Number of peptides per proteins plot
#17
IgnatiusPang
closed
2 weeks ago
0
Percentage of samples with values per protein bar plot
#16
IgnatiusPang
opened
2 months ago
0
Number of peptides and proteins per sample bar plot
#15
IgnatiusPang
closed
2 months ago
1
Extract GO terms from uniprot annotations for clusterProfiler
#14
Bucket-Chemist
opened
2 months ago
0
Automatically run uniprot annotations
#13
Bucket-Chemist
closed
2 weeks ago
0
Tidy up all the results folder allocation and output file names
#12
Bucket-Chemist
opened
2 months ago
0
Tidy up merged RLE PCA composite figure and auto align x and y axis limits
#11
Bucket-Chemist
closed
2 weeks ago
0
Function to print list of PCA plots with dots coloured by different column in design matrix. Reuse logic from RLE plots
#10
Bucket-Chemist
closed
2 months ago
1
Use % of total dataset to pick k for ruviii-c (set as a param up top)
#9
Bucket-Chemist
opened
2 months ago
0
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