BitSeq 1.0 wishlist
Antti Honkela edited this page Feb 11, 2015
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1 revision
- better DE
- new fold-change-based statistic
- FDR
- gene-level output included by default
- test for absolute and relative transcript abundance changes
- consistent gene and transcript-level analyses (single transcript genes should behave the same as the corresponding transcript)
- improved command line interface: single binary program, actions as verbs (cf. git, samtools, ...)
- rationale: easier to install system-wide
- improved file formats: include transcript names in all result files
- rationale: help prevent errors in interpretation of the results
- improved paired-end distance estimation
- better likelihood for indels
- better bias models from multiple samples
- a clear interface for models would be good