版本1.5（开发版本） +选择一个更合理的量表，用于全局过度分散估计 +使代码更强大的意外内部NA的 +添加后备机制，以防Fisher得分无法收敛。而不是重新进行NA，而是使用BFGS算法重试。+更好的错误消息如果设计包含NA的1.4版（2021-05-19） + Ridge正则化框架。Glmgampoi现在支持使用二次惩罚函数正规化系数估计值。此外，还实施了更高级的正规化方案，例如正规化特定价值和全蒂克霍诺夫正规化。+ new Predive（）函数。还支持估计平均估计值的标准误差。+确保Fisher评分不会收敛于MU +修复次要错误的不切实际值（）test_de（）中的次要错误，以计算自由程度 +修复次要错误在计算工作和Pearson残留物中的次要错误，如果MU如果MU，则返回NAN现在为0。它们是0。 +改进的小插图/读数：与Kang等人有关差异表达分析的章节。（2018）作为示例数据 +`glm_gp`返回偏移矩阵和bug修复test_de（）如果指定了偏移量 +添加引用文件 +确保残留是原始的（输入为延迟时） +残差的dimnames + Improve error message if input is a sparse matrix Version 1.2 (2020-11-09) + Remove dual likelihood functions for overdispersion estimation. Instead merge functionality into conventional_***. This should cause no user facing changes, however should make it easier to maintain the package + Make conventional_score_function_fast() more robust to extreme inputs. Avoid numerically imprecise subtractions and employ bounds based on series expansions for very small input + If dispersion estimate quits because there is no maximum or all y are 0, return iterations = 0 + Add limits (1e-16 / 1e16) for nlminb estimates of the dispersion. This protects against errors due to NA's in the conventional_likelihood_fast + Automatically set 'size_factors = FALSE' for input with 0 or 1 row. This will change the estimated beta, but not the mu's + Rename gampoi_overdispersion_mle() -> overdispersion_mle() + Store data in the object returned by glm_gp() + Remove Y from the interface of residuals.glmGamPoi, because I can just get it directly from fit$data + Add function test_de() that does a quasi-likelihood ratio test to detect differentially expressed genes + Add functionality to make a pseudobulk test directly from test_de() by aggregating the data around one column + In group-wise beta estimation, fall back to optimize() if the Newton method fails + Change the default size factor estimation method from "poscounts" to "normed_sum" and provide an easy way to call scran::calculateSumFactors() + New "global" mode for dispersion estimation Changes in version 0.0.99 (2020-03-23) + Submitted to Bioconductor