ejh243/BrainFANS

Issues

• [Code Refactor]: only run cortical clock for brain samples

  #229 opened a month ago by ew367
  0

• [Bug]: Full git tag is shown on QC rmd report

  #226 opened a month ago by sof202
  1

• [Enhancement suggestion]: QC report add document code version

  #211 opened a month ago by ejh243
  0

• [Enhancement suggestion]: GitHub description

  #225 opened a month ago by sof202
  2

• [Bug]: QC Report Section 4.2 reconfirming genetic relationships

  #214 opened a month ago by Molly-Endicott
  0

• [Code Refactor]: Multiple variables currently exist for same data (Sentrix_ID and _Position)

  #224 opened a month ago by ew367
  0

• [Enhancement suggestion]: Adapt checkColnamesSampleSheet.r script to check that all basenames are unique

  #223 opened a month ago by ew367
  1

• [Enhancement suggestion]: Remove techVar and bioVar variables and replace with hardcoded Sentrix_ID and Sentrix_Position and optional project variables (projVar)

  #216 opened a month ago by ew367
  2

• [Bug]: installLibraries.r script contains errors and is missing libraries essential to run QC.rmd

  #221 opened a month ago by ew367
  0

• [Bug]: Principal component analysis for autosomal probes

  #195 opened a month ago by Molly-Endicott
  2

• [Bug]: clusterCellTypes.r script doesn't work when phenotype info is not available

  #198 opened 2 months ago by ew367
  1

• [Enhancement suggestion]: update dasen to dasen.adj

  #210 opened a month ago by ejh243
  1

• [Code Refactor]: PBS usage

  #161 opened 3 months ago by sof202
  0

• [Bug]: r config file incorrectly specificed in config template

  #176 opened 2 months ago by ejh243
  1

• Extracting chromosome and design type from EPIC V1 manifest in ctCheck.rmd

  #185 opened 2 months ago by AnthonyKl98
  1

• [Bug]: technical variables summary never shows

  #188 opened a month ago by sof202
  2

• [Enhancement suggestion]: qual summary stats

  #212 opened a month ago by ejh243
  1

• [Enhancement suggestion]: Add stops on unsuccessful scripts

  #213 opened a month ago by sof202
  0

• [Enhancement suggestion]: Check variables exist before execution

  #184 opened a month ago by ejh243
  1

• [Enhancement suggestion]: Pfilter for probe removal

  #192 opened 2 months ago by eld211
  2

• [Bug]: config.example.r file is missing "arrayType" variable parameter

  #201 opened a month ago by ew367
  3

• [Code Refactor]: installLibraries.r script contains unecessary code

  #199 opened 2 months ago by ew367
  2

• [Documentation Fault]: Docusaurus is outdated

  #162 opened 2 months ago by sof202
  0

• [Code Refactor]: nested c() calls

  #181 opened 2 months ago by sof202
  0

• [Code Refactor]: messy conditional logic in CETYGOdeconvolution.r

  #186 opened 2 months ago by sof202
  0

• [Bug]: Bug in QC.rmd from microarray QC pipeline

  #196 opened 2 months ago by dmsoanes
  1

• [Bug]: miscalculating genetically unique individuals in the QC report

  #193 opened 2 months ago by Molly-Endicott
  1

• [Bug]: DNAm install libraries script not working on clean install

  #164 opened 2 months ago by sof202
  1

• [Bug]: Possible bug in QC.rmd script in DNAm QC pipeline

  #173 opened 2 months ago by dmsoanes
  4

• [Bug]: Possible bug in QC.rmd script in DNA microarray QC pipeline

  #177 opened 2 months ago by dmsoanes
  4

• [Bug]: Possible bug in QC.rmd script in DNA microarray QC pipeline

  #179 opened 2 months ago by dmsoanes
  3

• [Bug]: `cellType` is not defined in CETYGOdeconvolution.R

  #183 opened 2 months ago by sof202
  1

• [Bug]: Error in example config file config.example.r (microarray QC)

  #171 opened 2 months ago by dmsoanes
  0

• [Bug]: Turn off clusterCellTypes script for non-cellsorted data

  #169 opened 2 months ago by ejh243
  0

• Missing Cell_Type column from sample sheet in DNAm QC

  #167 opened 3 months ago by ejh243
  0

• [Enhancement suggestion]: Use of renv to manage packages

  #166 opened 3 months ago by ejh243
  0

• [Bug]: V2 Probe names need to be cleaned before EWAS

  #165 opened 3 months ago by rhaigh5
  0

• [Bug]: CountMTReads not generating properly, escape sequences not recognised

  #157 opened 4 months ago by sof202
  3

• [Documentation Fault]: encourage use of `git pull --rebase`

  #136 opened 4 months ago by sof202
  0

• [Code Refactor]: Unneeded download files

  #156 opened 4 months ago by sof202
  1

• [Code Refactor]: Possible temporary file

  #155 opened 4 months ago by sof202
  0

• [Enhancement suggestion]: Add parameters config file

  #154 opened 4 months ago by marinafloresp
  0

• [Enhancement suggestion]: Add QC step after trimming and before alignment

  #147 opened 4 months ago by marinafloresp
  0

• [Bug]: FASTP detecting adapters but not trimming

  #148 opened 4 months ago by marinafloresp
  0

• [Enhancement suggestion]: Add installLibraries script to README/pipeline

  #141 opened 5 months ago by ejh243
  0

• [Bug]: DNAm QC pipeline sex check thresholds

  #152 opened 5 months ago by ejh243
  0

• [Bug]: add scripts directory variable to config

  #137 opened 5 months ago by ejh243
  0

• Install libraries at start of QC[Bug]:

  #145 opened 5 months ago by rhaigh5
  4

• [Documentation Fault]: Incorrect `git reset` command

  #144 opened 5 months ago by sof202
  0

• [Bug] calcQCmetrics nFACS giving N/As

  #138 opened 6 months ago by AnthonyKl98
  0