P-value aggregation and many bugfixes
version 0.30.0
This version integrates p-value aggregation as described in Yi et al..
The behavior of gene-level differential expression testing now follows this procedure:
- Isoform-level testing.
- P-value aggregation at the gene level (using
target_mapping) by the lancaster method.
Thank you to Lynn Yi for implementing p-value aggregation.
Please see pull request #148 for details.
The API has also slightly changed. Particularly, for sleuth_prep, several options have been moved to optional arguments via .... See pull request #168 for more information or ?sleuth_prep in R.
A fair amount of speed up and bug fixes have also been implemented.
- Patch: bugs in sleuth_results & other miscellaneous fixes
- Fix behavior of sleuth_results when gene_mode is TRUE (and error reporting)
- Shiny and Plot Fixes / Enhancements
- Quick Patch: UseMethod typo
- Update
write_kallisto_hdf5function and add ability to subset kallisto object (address #131) - extend sleuth to model TPMs
- Fixes to various miscellaneous issues (#73, #84, #97, #122, #135, #142)
- Improvements to shiny and plot functions (solving several open issues)
- Possible solution to NAs in sleuth_lrt, addressing #68
- bug fix patches
- address #113 - patch bug where TPM bootstrap summary target_ids are moved
- New tests for ".N" target mappings
- Misc bug fixes + Allow sleuth_prep to process just one sample
A major thanks to Warren McGee for doing the majority of the heavy lifting on all of the bug fixes.