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ejh243
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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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[Bug]: Possible bug in QC.rmd script in DNA microarray QC pipeline
#179
dmsoanes
closed
1 month ago
3
refactor: convert section "definPlotParams" into functions
#178
sof202
closed
1 month ago
2
[Bug]: Possible bug in QC.rmd script in DNA microarray QC pipeline
#177
dmsoanes
closed
1 month ago
4
[Bug]: r config file incorrectly specificed in config template
#176
ejh243
opened
1 month ago
1
166 enhancement suggestion use of renv to manage packages
#175
ejh243
opened
1 month ago
9
feat: add stop call to error message in QC.rmd
#174
sof202
closed
1 month ago
2
[Bug]: Possible bug in QC.rmd script in DNAm QC pipeline
#173
dmsoanes
closed
1 month ago
4
fix: Enforce Boolean value for cellSorted
#172
sof202
closed
1 month ago
0
[Bug]: Error in example config file config.example.r (microarray QC)
#171
dmsoanes
closed
1 month ago
0
169 bug turn off clustercelltypes script for non cellsorted data
#170
ejh243
closed
1 month ago
0
[Bug]: Turn off clusterCellTypes script for non-cellsorted data
#169
ejh243
closed
1 month ago
0
filter to columns that exist before subsetting
#168
ejh243
closed
1 month ago
0
Missing Cell_Type column from sample sheet in DNAm QC
#167
ejh243
closed
1 month ago
0
[Enhancement suggestion]: Use of renv to manage packages
#166
ejh243
opened
2 months ago
0
[Bug]: V2 Probe names need to be cleaned before EWAS
#165
rhaigh5
opened
2 months ago
0
[Bug]: DNAm install libraries script not working on clean install
#164
sof202
closed
1 month ago
1
Resolve high severity vulnerabilities
#163
sof202
closed
3 weeks ago
0
[Documentation Fault]: Docusaurus is outdated
#162
sof202
closed
3 weeks ago
0
[Code Refactor]: PBS usage
#161
sof202
opened
2 months ago
0
Update ATAC-seq pipeline with latest working scripts
#160
marinafloresp
opened
2 months ago
1
Remove missing_package_linter
#159
sof202
closed
1 month ago
0
Add escape sequence interpretability to countMTReads.txt header row
#158
sof202
closed
2 months ago
0
[Bug]: CountMTReads not generating properly, escape sequences not recognised
#157
sof202
closed
2 months ago
3
[Code Refactor]: Unneeded download files
#156
sof202
opened
3 months ago
1
[Code Refactor]: Possible temporary file
#155
sof202
opened
3 months ago
0
[Enhancement suggestion]: Add parameters config file
#154
marinafloresp
opened
3 months ago
0
Use full file paths instead of globs in s/f tests
#153
sof202
closed
3 weeks ago
0
[Bug]: DNAm QC pipeline sex check thresholds
#152
ejh243
opened
3 months ago
0
126 enhancement suggestion turn off cell type clustering if bulk tissue
#151
ejh243
closed
2 months ago
3
Cell ewas methods
#150
ejh243
closed
2 months ago
2
Config file examples for pipeline
#149
marinafloresp
closed
2 months ago
4
[Bug]: FASTP detecting adapters but not trimming
#148
marinafloresp
closed
3 months ago
0
[Enhancement suggestion]: Add QC step after trimming and before alignment
#147
marinafloresp
closed
3 months ago
0
Update advice to reliably correct commits being made to master
#146
sof202
closed
4 months ago
0
Install libraries at start of QC[Bug]:
#145
rhaigh5
closed
3 months ago
4
[Documentation Fault]: Incorrect `git reset` command
#144
sof202
closed
4 months ago
0
Add advice to guide on using the `--rebase` flag when pulling
#143
sof202
closed
2 months ago
1
remove namespace_linter
#142
sof202
closed
4 months ago
0
[Enhancement suggestion]: Add installLibraries script to README/pipeline
#141
ejh243
closed
3 months ago
0
as.character(sample IDs) so nFACS no longer gives N/As
#140
AnthonyKl98
closed
4 months ago
0
137 bug add scripts directory variable to config
#139
ejh243
closed
3 months ago
5
[Bug] calcQCmetrics nFACS giving N/As
#138
AnthonyKl98
closed
4 months ago
0
[Bug]: add scripts directory variable to config
#137
ejh243
closed
3 months ago
0
[Documentation Fault]: encourage use of `git pull --rebase`
#136
sof202
closed
2 months ago
0
Normalisation script Cell.type vs Cell_Type[Bug]:
#135
AnthonyKl98
closed
3 months ago
2
change linters used
#134
sof202
closed
4 months ago
0
[Code Refactor]: lintr is picking up on too many stylistic lints
#133
sof202
closed
4 months ago
0
[Bug]: For age correlation stats missing check for variable age
#132
ejh243
closed
4 months ago
0
verify columns needed are in data frame
#131
ejh243
closed
4 months ago
0
[Bug]: QC.rmd expects genoCheck column if snpCheck = TRUE
#130
ejh243
closed
4 months ago
0
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