atacseq_analysis merge requestshttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests2020-07-01T14:35:42-05:00https://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/29Add in astrocyte 0.3.1 test.2020-07-01T14:35:42-05:00Venkat MalladiAdd in astrocyte 0.3.1 test.Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- ...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] `CHANGELOG.md` is updated
Closes #41Version 2.1.0Jonathan GesellJonathan Gesellhttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/26Resolve "Annotate peaks"2020-06-11T16:18:58-05:00Holly RuessResolve "Annotate peaks"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
Closes #32Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/25Resolve "Blacklist of regions"2020-06-09T14:55:50-05:00Holly RuessResolve "Blacklist of regions"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
Closes #31 Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/24Resolve "Add fragment size distribution"2020-06-09T09:15:49-05:00Venkat MalladiResolve "Add fragment size distribution"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
Closes #27Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/23WIP: Resolve "Add fragment size distribution"2020-06-02T09:33:02-05:00Holly RuessWIP: Resolve "Add fragment size distribution"Closes #27Closes #27Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/22Resolve "TSS enrichment score"2020-05-28T20:56:03-05:00Venkat MalladiResolve "TSS enrichment score"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
Closes #30Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/21Resolve "TSS enrichment score"2020-05-28T08:08:54-05:00Holly RuessResolve "TSS enrichment score"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
Closes #30Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/20Resolve "Add FRiP score"2020-05-13T09:30:50-05:00Venkat MalladiResolve "Add FRiP score"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
Closes #29Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/19Resolve "Add FRiP score"2020-05-13T09:24:44-05:00Holly RuessResolve "Add FRiP score"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [ ] This comment contains a description of changes (with reason)
- [ ] If you've fixed a bug or added code that should be tested, add tests!
- [ ] Documentation in `docs` is updated
- [ ] `CHANGELOG.md` is updated
- [ ] `README.md` is updated
- [ ] `LICENSE.md` is updated with new contributors
Closes #29Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/16Resolve "Add percent of reads - mitochondria"2020-03-24T14:23:38-05:00Holly RuessResolve "Add percent of reads - mitochondria"Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)...Please fill in the appropriate checklist below (delete whatever is not relevant).
These are the most common things requested on pull requests (PRs).
## PR checklist
- [x] This comment contains a description of changes (with reason)
- [x] If you've fixed a bug or added code that should be tested, add tests!
- [x] Documentation in `docs` is updated
- [x] `CHANGELOG.md` is updated
- [x] `README.md` is updated
Closes #28Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/15Resolve "Generate MultiQC report"2020-02-25T07:45:39-06:00Holly RuessResolve "Generate MultiQC report"Closes #26Closes #26Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/14Resolve "Fix BioHPC config"2020-01-07T09:38:50-06:00Holly RuessResolve "Fix BioHPC config"Closes #25Closes #25Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/13Resolve "fix consensus peaks"2020-01-07T09:35:32-06:00Holly RuessResolve "fix consensus peaks"Closes #24Closes #24Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/12Resolve "Fix Pool and Pseudoreps"2020-01-03T08:47:15-06:00Holly RuessResolve "Fix Pool and Pseudoreps"Closes #20
Closes #19Closes #20
Closes #19Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/11Resolve "Fix Convert Reads"2019-12-27T14:34:29-06:00Holly RuessResolve "Fix Convert Reads"Closes #18Closes #18Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/10Resolve "Fix Experiment QC"2019-12-20T10:28:15-06:00Holly RuessResolve "Fix Experiment QC"Closes #17Closes #17Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/9fix filter reads2019-12-18T08:03:53-06:00Holly Ruessfix filter readsCloses #15Closes #15Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/8Resolve "Fix Align Reads"2019-12-16T17:14:33-06:00Holly RuessResolve "Fix Align Reads"Closes #16Closes #16Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/7Resolve "Fix Trim Reads"2019-12-11T08:23:16-06:00Venkat MalladiResolve "Fix Trim Reads"Closes #14Closes #14Version 2.0Venkat MalladiVenkat Malladihttps://git.biohpc.swmed.edu/BICF/Astrocyte/atacseq_analysis/-/merge_requests/6WIP: Resolve "Fix Trim Reads"2019-12-11T08:17:26-06:00Holly RuessWIP: Resolve "Fix Trim Reads"Closes #14Closes #14Version 2.0Venkat MalladiVenkat Malladi