Man pages for Sun-lab/CARseq
Cell type-specific differential analysis of count data
| barplot_3d | Generate 3d barplot. |
| CARseq-package | CARseq package for cell type-specific differential analysis... |
| estimate_shrinkage_prior | Estimate the prior needed for LFC shrinkage |
| estimate_variance_parameter | Estimate variance parameter of zero-mean normal prior based... |
| fit_model | fit a CARseq negative binomial model using iteratively... |
| get_qvalues_one_inflated | Calculate q-values (Storey 2003) from a p-value distribution... |
| grad_negloglik | Gradient of negative log-likelihood of a negative binomial... |
| n50DE221rep1 | A simulated dataset of read counts of 50 samples and 10,000... |
| negloglik | negative log-likelihood function of a CARseq negative... |
| negloglik_adjusted_profile | negative adjusted profile log-likelihood function of a CARseq... |
| permute_case_and_controls | Permute case and control labels symmetrically |
| run_CARseq | Conduct a CARseq test |
