diff --git a/README.mkd b/README.mkd index 8f629f4..7ad5aba 100644 --- a/README.mkd +++ b/README.mkd @@ -132,7 +132,7 @@ usage: genipe-launcher [-h] [-v] [--debug] [--thread THREAD] --bfile PREFIX [--report-background BACKGROUND] Execute the genome-wide imputation pipeline. This script is part of the -'genipe' package, version 1.3.1. +'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit @@ -277,7 +277,7 @@ usage: imputed-stats [-h] [-v] {cox,linear,logistic,mixedlm,skat} ... Performs statistical analysis on imputed data (either SKAT analysis, or linear, logistic or survival regression). This script is part of the 'genipe' -package, version 1.3.1. +package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/index.rst b/docs/index.rst index 9dfebb0..475f735 100644 --- a/docs/index.rst +++ b/docs/index.rst @@ -69,7 +69,7 @@ Usage [--report-background BACKGROUND] Execute the genome-wide imputation pipeline. This script is part of the - 'genipe' package, version 1.3.1. + 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/installation.rst b/docs/installation.rst index f9d22e4..8eb05f7 100644 --- a/docs/installation.rst +++ b/docs/installation.rst @@ -29,6 +29,11 @@ management): * ``pyfaidx`` version 0.3.7 or latest * ``drmaa`` version 0.7.6 or latest +.. note:: + + Note that ``statsmodels`` (specifically MixedLM analysis) version 0.6 + **is not compatible** with ``numpy`` version 1.12 and latest. + .. note:: Only Python version 3.4 and higher are supported. diff --git a/docs/tutorials/tutorial_SKAT.rst b/docs/tutorials/tutorial_SKAT.rst index aec2992..56e3060 100644 --- a/docs/tutorials/tutorial_SKAT.rst +++ b/docs/tutorials/tutorial_SKAT.rst @@ -334,7 +334,7 @@ the console: {continuous,discrete} [--skat-o] --pheno-name NAME Uses the SKAT R package to analyze user defined gene sets. This script is part - of the 'genipe' package, version 1.3.1. + of the 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/tutorials/tutorial_cox.rst b/docs/tutorials/tutorial_cox.rst index 8898934..5459c01 100644 --- a/docs/tutorials/tutorial_cox.rst +++ b/docs/tutorials/tutorial_cox.rst @@ -222,7 +222,7 @@ in the console: NAME Performs a survival regression on imputed data using Cox's proportional hazard - model. This script is part of the 'genipe' package, version 1.3.1. + model. This script is part of the 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/tutorials/tutorial_extract.rst b/docs/tutorials/tutorial_extract.rst index 01eb22c..3cbe553 100644 --- a/docs/tutorials/tutorial_extract.rst +++ b/docs/tutorials/tutorial_extract.rst @@ -237,7 +237,7 @@ analysis in the console: [--rate FLOAT] [--info FLOAT] Extract imputed markers located in a specific genomic region. This script is - part of the 'genipe' package, version 1.3.1. + part of the 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/tutorials/tutorial_linear.rst b/docs/tutorials/tutorial_linear.rst index 9465128..e99f6d4 100644 --- a/docs/tutorials/tutorial_linear.rst +++ b/docs/tutorials/tutorial_linear.rst @@ -235,7 +235,7 @@ analysis in the console: --pheno-name NAME Performs a linear regression (ordinary least squares) on imputed data. This - script is part of the 'genipe' package, version 1.3.1. + script is part of the 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/tutorials/tutorial_logistic.rst b/docs/tutorials/tutorial_logistic.rst index b4fde9c..cbb500a 100644 --- a/docs/tutorials/tutorial_logistic.rst +++ b/docs/tutorials/tutorial_logistic.rst @@ -224,7 +224,7 @@ regression analysis in the console: --pheno-name NAME Performs a logistic regression on imputed data using a GLM with a binomial - distribution. This script is part of the 'genipe' package, version 1.3.1. + distribution. This script is part of the 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit diff --git a/docs/tutorials/tutorial_mixedlm.rst b/docs/tutorials/tutorial_mixedlm.rst index 6787a79..f2f4898 100644 --- a/docs/tutorials/tutorial_mixedlm.rst +++ b/docs/tutorials/tutorial_mixedlm.rst @@ -266,7 +266,7 @@ effects analysis in the console: Performs a linear mixed effects regression on imputed data using a random intercept for each group. A p-value approximation is performed so that computation time is acceptable for imputed data. This script is part of the - 'genipe' package, version 1.3.1. + 'genipe' package, version 1.3.2. optional arguments: -h, --help show this help message and exit