genipe - Version 1.5.0

This version uses Python 3.7 and up, and it should work will the newest versions of all the dependencies.

- Python
Published by lemieuxl about 5 years ago

genipe - Version 1.4.2

Newer versions of lifelines raise a ValueError when the algorithm can't converge. This version of genipe now catches this error and warns the user (instead of quitting).

- Python
Published by lemieuxl over 7 years ago

genipe - Version 1.4.1

Fixed an issue when launching jobs with DRMAA and the "start time" or "end time" of the job wasn't reported. If "start time" is missing, it is replaced by the "launch time". If the "end time" is missing, it is replaced by the current time when DRMAA returned the job as completed.

This version of genipe should now work with the most recent versions of the different python modules. It has been tested with the following versions:

| Module | Minimal tested version | Tested up to | | :--- | ---: | ---: | | numpy | 1.11.3 | 1.14.3 | | pandas | 0.19.2 | 0.23.0 | | lifelines | 0.12.0 | 0.14.3 | | statsmodels | 0.8.0 | 0.9.0 |

- Python
Published by lemieuxl almost 8 years ago

genipe - Version 1.4.0

This version of genipe should work with the most recent versions of the different python modules. It has been tested with the following versions:

| Module | Minimal tested version | Tested up to | | :--- | ---: | ---: | | numpy | 1.11.3 | 1.13.3 | | pandas | 0.19.2 | 0.21.0 | | lifelines | 0.12.0 | 0.12.0 |

- Python
Published by lemieuxl about 8 years ago

genipe - Version 1.3.3

The tutorial script was updated: * Checks binaries in the system path before downloading them. * Updated link to download Plink.

Because of the different module's deprecation, this release should work only with the following module's version. Newer versions wouldn't work with this release of genipe. * pandas version 0.19 * lifelines version 0.9

- Python
Published by lemieuxl almost 9 years ago

genipe - Version 1.3.2

This release includes the following changes: - Compatibility with statsmodels version 0.8.0. - Conda package for Python 3.6.

- Python
Published by lemieuxl about 9 years ago

genipe - Version 1.3.1

This release includes the following changes: - When launching the pipeline, using --chrom autosomes will now launch the analysis on all autosomes (from chromosomes 1 to 22). - The tutorial script (genipe-tutorial) now performs the analysis on the autosomes.

- Python
Published by lemieuxl over 9 years ago

genipe - Version 1.3.0

Changes to the main imputation pipeline include: - Can now impute only a subset of chromosomes (the --chrom option). - Possibility to further customize SHAPEIT (the --shapeit-extra option). - Possibility to further customize IMPUTE2 (the --impute2-extra option). - Chromosome X (both pseudo- and non-pseudo-autosomal regions) are now imputable.

Changes to the statistical tool include: - Mixed linear model is now optimized to significantly reduce computation time. - Better handling of categorical variables in survival analysis (CoxPH) (the --categorical option). - Linear analysis now returns the adjusted r-squared value.

Changes to the extraction tool include: - Addition of the LGEN output format (the --long option, available for the calls and dosage format). - Addition of the BED output format (the --format bed option).

The compatibility with Python 3.3 was removed (since pandas versions are too old in anaconda for this version).

- Python
Published by lemieuxl over 9 years ago

genipe - Version 1.2.3

Changes include: - A standalone script that downloads reference files, genotype files and binaries to help the user execute the main pipeline tutorial (be sure to check the binaries licences (see here for more information). - Better documentation.

- Python
Published by lemieuxl almost 10 years ago

genipe - Version 1.2.2

Changes include: - Automatic report - creates a bar plot instead of a pie chart for better frequency comparison - minor amelioration in the template (for file names) - option (--report-background) to change the content of the background section - impute2-extractor - possible to only index impute2 files using --index - when extracting in impute2 format, the companion files are also processed - corrected some tests that failed depending of system used

- Python
Published by lemieuxl over 10 years ago

genipe - Version 1.2.1

This release fixes the following bugs: - Issue #14, where an exception was raised for launching to many event client listener on SGE using DRMAA. - Issue #15, where an exception was raised while compiling execution time for the automatic report and there are missing time for failed bgzip compression.

- Python
Published by lemieuxl over 10 years ago

genipe - Version 1.2.0

This new release of our genome-wide imputation pipeline includes the following changes: - The impute2-merger tool now merges the marker-wise information file produced for each segment (*.impute2_info) into a single file (in the final_impute2 directory of each chromosome). - The impute2-extractor tool can now extract markers according to their information value (along with other metrics, such as genomic locations, minor allele frequency and call rate). - Minor bug fixed in the impute2-extractor tool, where minor allele frequency was computed using all probabilities instead of filtering out values lower than the specified threshold.

In brief, this release now takes into account the information file provided by IMPUTE2. This information file includes the measure of the observed statistical information associated with the allele frequency estimate. More information about this metric is available here.

- Python
Published by lemieuxl over 10 years ago

genipe - Version 1.1.0

This is the second release of our genome-wide imputation pipeline (version 1.1.0). Here is the list of the changes: - The package has been renamed to genipe (for GENome-wide Imputation PipelinE). - Linear mixed effects models (for repeated measures) has been added to the imputed-stats tool (click here for more information). - More tests have been added to the test suite (mostly for the linear mixed effects model). - Documentation has been improved and updated for this release. The documentation is available here.

Complete documentation is available at http://pgxcentre.github.io/genipe

Installation: http://pgxcentre.github.io/genipe/installation.html

Tutorials: http://pgxcentre.github.io/genipe/tutorials.html

- Python
Published by lemieuxl over 10 years ago

genipe - Version 1.0.0

This is the initial release of gwip (Genome-Wide Imputation Pipeline). Interesting features include: - Complete and automatic genome-wide imputation pipeline from binary Plink files. Steps include: - strand verification - phasing - imputation - quality metrics - All analysis are performed by chromosome and can be launch on an computer cluster using the DRMAA API (if required). - Automatically generates a LaTeX report that can be compiled in PDF format. - Commonly used statistical analysis - linear regression - logistic regression - SKAT analysis - survival analysis (Cox’s proportional hazard model) - Indexing of file for easy imputed marker extraction

Complete documentation is available at http://pgxcentre.github.io/gwip

Installation: http://pgxcentre.github.io/gwip/installation.html

Tutorials: http://pgxcentre.github.io/gwip/tutorial.html

- Python
Published by lemieuxl almost 11 years ago