Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / lieberinstitute/biocmap issues and pull requests

#30 - [FEATURE REQUEST] Allow user configuration of Arioc's "<A>" element

Issue - State: open - Opened by Nick-Eagles over 1 year ago - 1 comment

#29 - Excessive memory required in `MergeBsseqObjects`

Issue - State: open - Opened by Nick-Eagles over 1 year ago

#28 - Add bioRxiv info

Issue - State: closed - Opened by lcolladotor almost 2 years ago

#27 - Update Test Data

Issue - State: closed - Opened by Nick-Eagles almost 3 years ago

#26 - Inefficient use of AriocE

Issue - State: closed - Opened by Nick-Eagles almost 3 years ago

#25 - Generate R Markdown for example FlowRNA-WGBS analysis

Issue - State: closed - Opened by Nick-Eagles about 3 years ago

#23 - Missing installation-related documentation and unsolved cases

Issue - State: closed - Opened by Nick-Eagles about 3 years ago - 1 comment

#22 - Add support for `--use_bme` with test files

Issue - State: closed - Opened by Nick-Eagles over 3 years ago

#20 - Add support for and document pipeline sharing

Issue - State: closed - Opened by Nick-Eagles over 3 years ago

#19 - Create docker images

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 2 comments

#18 - Bismark genome preparation should be performed conditionally

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 1 comment

#17 - `rules.txt` does not specify filenames strictly enough

Issue - State: closed - Opened by Nick-Eagles over 3 years ago

#16 - Optimize methylation extraction with MethyDackel

Issue - State: open - Opened by Nick-Eagles over 3 years ago

#15 - Add "local" and "jhpce" arguments to the installation script

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 1 comment

#14 - Untrimmed uncompressed FASTQ files are published as outputs

Issue - State: closed - Opened by Nick-Eagles over 3 years ago - 1 comment

#13 - Parsing of Arioc logs assumed paired-ness of data

Issue - State: closed - Opened by Nick-Eagles almost 4 years ago

#12 - Fix incorporation of methylation metrics

Issue - State: closed - Opened by Nick-Eagles almost 4 years ago

#11 - `FilterAlignments` and `SamToBam` should be combined

Issue - State: closed - Opened by Nick-Eagles almost 4 years ago

#10 - Outputs are not logically organized

Issue - State: closed - Opened by Nick-Eagles almost 4 years ago

#9 - Merge output bsseq objects and metrics data frame

Issue - State: closed - Opened by Nick-Eagles almost 4 years ago

#8 - Incorporate FastQC metrics in output data frame

Issue - State: closed - Opened by Nick-Eagles about 4 years ago - 1 comment

#7 - Add configuration and "main" files for SLURM, SGE environments

Issue - State: closed - Opened by Nick-Eagles about 4 years ago - 1 comment

#6 - Allow user to specify genome files to use

Issue - State: closed - Opened by Nick-Eagles about 4 years ago

#5 - Test the "ParseReports" process

Issue - State: closed - Opened by Nick-Eagles over 4 years ago

#4 - Fix smoothing of CpG bsseq objects

Issue - State: closed - Opened by Nick-Eagles over 4 years ago

#3 - Encoded reads hog disk space

Issue - State: closed - Opened by Nick-Eagles over 4 years ago

#2 - Arioc alignment often fails due to starved GPU resources

Issue - State: closed - Opened by Nick-Eagles about 5 years ago - 2 comments