ejh243 BrainFANS issues

ejh243 / BrainFANS

Complex Disease Epigenomics Group's quality control and analysis pipelines for DNA methylation arrays, SNP arrays, BS-Seq, ATAC-Seq and ChIP-Seq

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issues

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[Documentation Fault]: Create contracts for each stage/section of DNAm QC pipeline

#259 sof202 opened 21 hours ago
1
[Documentation Fault]: Create a UML diagram explaining the steps for the DNAm QC pipeline

#258 sof202 opened 21 hours ago
0
[Code Refactor]: Orthogonalise the DNAm QC pipeline

#257 sof202 opened 21 hours ago
1
[Documentation Fault]: Add example sampleSheet files

#256 sof202 opened 4 days ago
0
[Documentation Fault]: Poor clarity in DNAm config files

#255 sof202 opened 4 days ago
0
[Documentation Fault]: Log/error files of DNAm QC pipeline are not user friendly

#253 sof202 opened 5 days ago
0
[Documentation Fault]: Repeated and incomplete information in README

#252 sof202 opened 6 days ago
0
fix: use 450K (capital) everywhere

#251 sof202 closed 1 week ago
0
fix: 450k consistency

#250 sof202 closed 1 week ago
0
[Bug]: 450k array type not loading manifest files

#249 sof202 closed 1 week ago
0
Add conda environment for DNAm QC dependencies installation

#248 sof202 opened 1 week ago
3
fix: use levels over unique

#247 sof202 opened 1 week ago
0
[Bug]: Plotting parameters legend mismatch

#246 sof202 opened 2 weeks ago
2
feat: add gridExtra to packages to installation script

#245 sof202 closed 20 hours ago
1
[Bug]: gridExtra not installed in installLibraries.r script

#244 lw371 closed 4 days ago
2
Move package installations

#243 sof202 closed 2 weeks ago
0
Fix annotation mismatch

#242 sof202 closed 1 week ago
0
[Bug]: EPIC V1 annotation file package version mismatch

#241 sof202 closed 1 week ago
0
[Bug]: QC installLibraries.R script will always fail

#240 sof202 closed 2 weeks ago
0
Update use of modules

#239 marinafloresp opened 2 weeks ago
0
[Bug]: Modules not working

#238 marinafloresp opened 2 weeks ago
0
Convert pbs

#237 sof202 opened 2 weeks ago
0
Cortical clock check

#236 sof202 closed 2 weeks ago
2
[Code Refactor]: create function to load and standardise manifests

#235 ew367 opened 3 weeks ago
1
add script to filter out sex specific probes

#234 ew367 closed 2 weeks ago
0
Add p filter for probe removal

#233 ew367 closed 1 week ago
0
Bump http-proxy-middleware from 2.0.6 to 2.0.7 in /documentation

#232 dependabot[bot] closed 4 weeks ago
0
Bump mermaid from 10.8.0 to 10.9.3 in /documentation

#231 dependabot[bot] closed 4 weeks ago
0
Bump cookie and express in /documentation

#230 dependabot[bot] closed 4 weeks ago
0
[Code Refactor]: only run cortical clock for brain samples

#229 ew367 closed 2 weeks ago
0
156 code refactor unneeded download files

#228 ejh243 opened 1 month ago
3
Make the git tag only show the version number

#227 sof202 closed 1 month ago
0
[Bug]: Full git tag is shown on QC rmd report

#226 sof202 closed 1 month ago
1
[Enhancement suggestion]: GitHub description

#225 sof202 closed 1 month ago
2
[Code Refactor]: Multiple variables currently exist for same data (Sentrix_ID and _Position)

#224 ew367 opened 1 month ago
0
[Enhancement suggestion]: Adapt checkColnamesSampleSheet.r script to check that all basenames are unique

#223 ew367 closed 1 month ago
1
add missing libraries and correct bug

#222 ew367 closed 1 month ago
4
[Bug]: installLibraries.r script contains errors and is missing libraries essential to run QC.rmd

#221 ew367 opened 1 month ago
0
Remove tech var and bio var variables

#220 ew367 closed 1 month ago
2
fix: PCs identified text showing incorrect number

#219 sof202 closed 1 month ago
0
fix: predictedduplicates containing empty strings

#218 sof202 closed 1 month ago
1
Add repository version to QC rmarkdown

#217 sof202 closed 1 month ago
2
[Enhancement suggestion]: Remove techVar and bioVar variables and replace with hardcoded Sentrix_ID and Sentrix_Position and optional project variables (projVar)

#216 ew367 closed 1 month ago
2
feat: Add more error logging to DNAm pipeline

#215 sof202 opened 2 months ago
3
[Bug]: QC Report Section 4.2 reconfirming genetic relationships

#214 Molly-Endicott closed 1 month ago
0
[Enhancement suggestion]: Add stops on unsuccessful scripts

#213 sof202 opened 2 months ago
0
[Enhancement suggestion]: qual summary stats

#212 ejh243 opened 2 months ago
1
[Enhancement suggestion]: QC report add document code version

#211 ejh243 closed 1 month ago
0
[Enhancement suggestion]: update dasen to dasen.adj

#210 ejh243 opened 2 months ago
1
refactor: checkRconfig

#209 sof202 closed 2 months ago
0