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41 Open 29 Closed
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Issues list

Add an intervene module
#199 opened May 23, 2025 by edmundmiller
Remove intermediate bams
#198 opened May 23, 2025 by edmundmiller
Turn off quality checks by default
#197 opened May 23, 2025 by edmundmiller
JSON schema: Nascent documentation
#192 opened Mar 25, 2025 by jen-reeve
15 tasks
Add license to bin scripts
#188 opened Jan 13, 2025 by edmundmiller
Add bed2tssbed conversion
#187 opened Jan 5, 2025 by edmundmiller
Report number of transcripts identified per method in MultiQC
#186 opened Dec 25, 2024 by edmundmiller 2.4.0
@edmundmiller
Clean up Publishing
#176 opened Nov 26, 2024 by edmundmiller
1 task done
2.4.0
groHMM fails with CHM13 occasionally bug Something isn't working
#172 opened Oct 21, 2024 by edmundmiller
@edmundmiller
Consider tsshmm enhancement New feature or request
#164 opened Sep 18, 2024 by edmundmiller
1
v.2.2.0 fails on multiple replicates of the same sample bug Something isn't working
#159 opened Aug 14, 2024 by dmitrymyl
6
Sample names must contain at least underscore (?) bug Something isn't working
#158 opened Aug 14, 2024 by dmitrymyl
1
Support not pooling reads for HOMER enhancement New feature or request
#153 opened Aug 3, 2024 by edmundmiller
Flakey test
#148 opened Jul 22, 2024 by edmundmiller
Issue with concatenation of technical replicates bug Something isn't working
#143 opened May 7, 2024 by bug1303
Discrepancy between bigwigs generated by bedtools and deeptools bug Something isn't working
#123 opened Oct 19, 2023 by Caffeinated-Code 2.4.0
1
@edmundmiller
Test results say chr22 when the ref is chr21? bug Something isn't working
#121 opened Sep 27, 2023 by edmundmiller
@edmundmiller
Flipped bigwig strands in PROseq samples
#115 opened Jun 29, 2023 by Caffeinated-Code
1
@edmundmiller
2
Bedtools sort output isn't deterministic bug Something isn't working
#102 opened Jan 19, 2023 by edmundmiller
Improve reporting when no transcripts are found enhancement New feature or request
#95 opened Oct 31, 2022 by edmundmiller
@edmundmiller
Example of 3D genome integration enhancement New feature or request
#93 opened Oct 26, 2022 by edmundmiller
motif production for region enhancement New feature or request
#92 opened Oct 26, 2022 by edmundmiller
Example of integration with ATAC-seq pipeline output enhancement New feature or request
#91 opened Oct 26, 2022 by edmundmiller
Support STAR enhancement New feature or request
#90 opened Oct 26, 2022 by edmundmiller
Clean up published files enhancement New feature or request
#89 opened Oct 25, 2022 by edmundmiller
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