Skip to content

Releases: pachterlab/sleuth

version 0.30.1

14 Nov 13:31
20e493f
Compare
Choose a tag to compare

P-value aggregation and many bugfixes

08 Jun 00:09
Compare
Choose a tag to compare

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:

  1. Isoform-level testing.
  2. 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.

A major thanks to Warren McGee for doing the majority of the heavy lifting on all of the bug fixes.

Improved speed and memory footprint

29 May 07:33
Compare
Choose a tag to compare

This version has numerous bug fixes and several performance upgrades.
Most notably, memory usage has been decreased greatly by no longer storing the bootstraps in memory.
Additionally, speed has been improved in numerous areas — particularly sleuth_prep — by changing several of the computations as well as changing the order of the parallelization (special thanks to Warren McGee for his contributions to this).

Below is an incomplete list of new features:

  • The full model no longer has to be specified in sleuth_prep.
  • A new function extract_model allow users to extract the effect sizes for a model in a tidy format similar to broom.
  • An arbitrary transformation can be specified/used in sleuth_prep (see argument transformation_function).

A big thanks to our users for fixing and reporting bugs.
A special thanks to Warren McGee for making several of the performance improvements as well as fixing several bugs.
Below is a partial list of many of the upgrades and the pull requests by the community.

Gene aggregation

20 Jun 22:17
Compare
Choose a tag to compare
  • Gene aggregation can now be performed via aggregation_column in sleuth_prep.
  • Documentation has improved
  • Vignette is updated
  • A few bugs have been fixed (plot_pca)

Likelihood ratio test, visualization, bug fixes, and more

28 Oct 16:59
Compare
Choose a tag to compare

There have been several changes including a very important bug fix. It is recommended that all users upgrade.

new features in the model

  • support for likelihood ratio test
  • support for arbitrary design matrices
  • support for arbitrary normalizations

bug fixes

  • sometimes the samples would get reordered based off of the sample names. This has been fixed.

miscellaneous

  • the interface of sleuth_prep has changed to encourage users to correctly specify the connection between samples, kallisto results, and covariates
  • imports fragment length distribution from kallisto
  • view the bias weights learned from kallisto
  • generalize reading from h5 allowing filename or directory to be specified

visualization and sleuth_live

  • most figures and tables can be saved directly from sleuth_live
  • fragment length distribution in sleuth_live
  • variance explained from principal components can be visualized
  • PCA loadings can now be visualized

Some updates to sleuth live

22 Oct 22:48
Compare
Choose a tag to compare
  • various bug fixes
  • gene table, gene viewer, transcript heatmap, and volcano plot by Pascal Sturmfels