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LieberInstitute
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BiocMAP
Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow
http://research.libd.org/BiocMAP/
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[FEATURE REQUEST] Allow user configuration of Arioc's "<A>" element
#30
Nick-Eagles
opened
1 year ago
1
Excessive memory required in `MergeBsseqObjects`
#29
Nick-Eagles
opened
1 year ago
0
Add bioRxiv info
#28
lcolladotor
closed
1 year ago
0
Update Test Data
#27
Nick-Eagles
closed
2 years ago
0
Inefficient use of AriocE
#26
Nick-Eagles
closed
1 year ago
0
Generate R Markdown for example FlowRNA-WGBS analysis
#25
Nick-Eagles
closed
2 years ago
0
Conda R executable seems to break after successful installation
#24
Nick-Eagles
opened
2 years ago
0
Missing installation-related documentation and unsolved cases
#23
Nick-Eagles
closed
2 years ago
1
Add support for `--use_bme` with test files
#22
Nick-Eagles
closed
3 years ago
0
Remove abuse of absolute paths and other workarounds that break docker mode
#21
Nick-Eagles
closed
3 years ago
0
Add support for and document pipeline sharing
#20
Nick-Eagles
closed
3 years ago
0
Create docker images
#19
Nick-Eagles
closed
3 years ago
2
Bismark genome preparation should be performed conditionally
#18
Nick-Eagles
closed
3 years ago
1
`rules.txt` does not specify filenames strictly enough
#17
Nick-Eagles
closed
3 years ago
0
Optimize methylation extraction with MethyDackel
#16
Nick-Eagles
opened
3 years ago
0
Add "local" and "jhpce" arguments to the installation script
#15
Nick-Eagles
closed
3 years ago
1
Untrimmed uncompressed FASTQ files are published as outputs
#14
Nick-Eagles
closed
1 year ago
1
Parsing of Arioc logs assumed paired-ness of data
#13
Nick-Eagles
closed
3 years ago
0
Fix incorporation of methylation metrics
#12
Nick-Eagles
closed
3 years ago
0
`FilterAlignments` and `SamToBam` should be combined
#11
Nick-Eagles
closed
3 years ago
0
Outputs are not logically organized
#10
Nick-Eagles
closed
3 years ago
0
Merge output bsseq objects and metrics data frame
#9
Nick-Eagles
closed
3 years ago
0
Incorporate FastQC metrics in output data frame
#8
Nick-Eagles
closed
3 years ago
1
Add configuration and "main" files for SLURM, SGE environments
#7
Nick-Eagles
closed
3 years ago
1
Allow user to specify genome files to use
#6
Nick-Eagles
closed
3 years ago
0
Test the "ParseReports" process
#5
Nick-Eagles
closed
3 years ago
0
Fix smoothing of CpG bsseq objects
#4
Nick-Eagles
closed
3 years ago
0
Encoded reads hog disk space
#3
Nick-Eagles
closed
3 years ago
0
Arioc alignment often fails due to starved GPU resources
#2
Nick-Eagles
closed
3 years ago
2
Arioc alignment should output good QNAME fields regardless of FASTQ read ID style
#1
Nick-Eagles
closed
4 years ago
1