Likelihood ratio test, visualization, bug fixes, and more

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