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QuackenbushLab
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NetworkDataCompanion
An R library of utilities for performing analyses on TCGA and GTEx data using the Network Zoo
GNU General Public License v3.0
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Updated documentation
#57
soelmicheletti
closed
3 days ago
0
adding workflow
#56
violafanfani
closed
3 days ago
0
addedd main
#55
violafanfani
closed
3 days ago
0
adding quickstart workflow
#54
violafanfani
closed
3 days ago
0
Renaming files to "NetworkDataCompanion"
#53
soelmicheletti
closed
3 days ago
0
R CMD check --as-cran
#52
katehoffshutta
opened
3 days ago
0
Renamed NetZooDataCompanion to NetworkDataCompanion
#51
soelmicheletti
closed
3 days ago
1
NetSci -> NetZoo name change
#50
katehoffshutta
closed
3 months ago
0
changes to build the package in introduction rmd
#49
violafanfani
closed
3 days ago
2
logCPM and logTPM are not coherent
#48
violafanfani
opened
6 months ago
3
Updated unit tests to address several issues on github
#47
katehoffshutta
closed
8 months ago
0
Unit test for inclusion of probes mapping to multiple genes and/or isoforms in mean promoter calculation
#46
katehoffshutta
closed
8 months ago
1
Add default gene names for probeToMeanPromoterMethylation
#45
katehoffshutta
opened
9 months ago
0
split to long form before filtering
#44
katehoffshutta
closed
9 months ago
0
Warning on function filterSampleType regarding a bracket
#43
pmandros
closed
8 months ago
2
UUID updates
#42
katehoffshutta
closed
9 months ago
0
ordering of gene identifiers in the gene* conversion functions
#41
katehoffshutta
opened
9 months ago
1
Support for ignoring NAs of individual probes in mean promoter methylation computation
#40
FischerJoBio
opened
1 year ago
2
Removed reassignment of first column of map to probe id; add NA for p…
#39
katehoffshutta
closed
1 year ago
0
Methylation probe mapping "Error in mymap[, 1] = probelist : number of items to replace is not a multiple of replacement length"
#38
FischerJoBio
closed
1 year ago
2
clinical_patient.csv testthat path
#37
cchen22
closed
8 months ago
1
Package Installation
#36
cchen22
opened
1 year ago
1
extractVialOnly has wrong indices
#35
katehoffshutta
closed
1 year ago
1
Rds_gene_info with duplicates
#34
soelmicheletti
opened
1 year ago
0
Argument of logCPMNormalization function
#33
soelmicheletti
closed
1 year ago
2
Specification of mapBarcodeToBarcode
#32
soelmicheletti
closed
1 year ago
1
reworked barcode filtering to avoid requiring RDS object; added tests
#31
katehoffshutta
closed
1 year ago
5
Removed legacy option and added exception if no UUIDs match to TCGA
#30
katehoffshutta
closed
1 year ago
0
updated probe mean methylation mapping docs and unit test
#29
katehoffshutta
closed
1 year ago
0
added doc outlines and huge dependency
#28
katehoffshutta
closed
1 year ago
0
Gene map ensembl ids are transcripts probeToMeanPromoterMethylation
#27
FischerJoBio
opened
1 year ago
4
Manual page for probeToMeanPromoterMethylation
#26
FischerJoBio
closed
1 year ago
1
switch to R-utils::gunzip
#25
katehoffshutta
closed
1 year ago
0
added default probe list for probe map generation
#24
katehoffshutta
closed
1 year ago
0
Gene name mapping
#23
katehoffshutta
closed
1 year ago
2
Added fix to subset syntax
#22
katehoffshutta
closed
1 year ago
0
mapUUIDtoTCGA legacy mode not available
#21
FischerJoBio
closed
1 year ago
1
remove long form probe map and add mean mapping from VF
#20
katehoffshutta
closed
1 year ago
0
function to map probes to genes and average methylation
#19
violafanfani
closed
1 year ago
1
changing depth filtering to include sample type
#18
violafanfani
closed
1 year ago
0
Duplicate removal should be done on sample and not the patient
#17
violafanfani
closed
1 year ago
6
add tcga barcodes; fix namespace
#16
katehoffshutta
closed
1 year ago
0
Sample mapping
#15
katehoffshutta
closed
1 year ago
0
Implement flexible slicing in methylation probe mapping
#14
katehoffshutta
opened
1 year ago
2
added testthat
#13
katehoffshutta
closed
1 year ago
0
Improve tumor type filtering
#12
katehoffshutta
closed
1 year ago
1
Add TMM normalization
#11
katehoffshutta
closed
2 years ago
1
Missing purity for some projects
#10
violafanfani
closed
2 years ago
1
extract sample type
#9
violafanfani
closed
2 years ago
0
Added more docs
#8
katehoffshutta
closed
2 years ago
0
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