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rbeagrie/BEAKER 2

Beaker Easily Analyzes the Kinetics of Enzyme Reactions

rbeagrie/bilbo_core 2

Bilbo is an automatic computational lab-book, based largely on bein and sumatra

rbeagrie/CurveFitting 2

A library containing some convenience functions for doing curve fitting in python

rbeagrie/2014-08-26-cam 1

University of Cambridge Software Carpentry Bootcamp - Aug 26/27 2014

rbeagrie/django-tmdb 1

A django app for displaying information from tmdb

akukalev/planets 0

Github workshop

rbeagrie/2016-03-23-Imperial 0

Website repo for Software Carpentry workshop held at Imperial College London on 23-24 March 2016.

rbeagrie/2016-03-23-Imperial-students 0

Repository for students to use/clone/fork during 23-24 March 2016 Software Carpentry workshop at ICL.

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PR opened pombo-lab/gamtools

Slice fix

Implement SLICE analysis code in GAMtools.

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Calculate coverage in bp rather than reads for subsequent thresholding (#32) * Calculate coverage in bp rather than reads for subsequent thresholding * Implemented orphan window based thresholding * Allow first/last windows to be orphans and fix pylint errors * Update help text for call_windows * Update CHANGELOG.md * Update CONTRIBUTORS.md

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Rob Beagrie

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Cython packaging (#35) * Distribute compiled .c extensions not .pyx source * Pre-install cython on travis * Don't warn about f-string usage * Fix pylint errors and bump version

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Rob Beagrie

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Fix issue with time.clock (#34) * Fix issue with time.clock * Switch from coveralls to codecov on travis

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Rob Beagrie

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Add fixed threshold option to process_nps command (#9) * Test for numpy handling boolean lists differently * Use boolean array not boolean list in filter_data

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Rob Beagrie

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Add option to use NPMI normalisation (#24) * scripts for npmi normalization, saturaction curves and new reads-coverage calculations Separated NPMI script * Added npmi as an option for matrix normalisation Co-authored-by: Alexander Kukalev <akukalev@gmail.com> Co-authored-by: Thomas Sparks <Thomas.Sparks@mdc-berlin.de> * Added tests for NPMI * Updated documentation * Bump version number * Fix problem with deprecated time.clock() function * Rely on pandas for matrix compression * Bump version number * Added contributors file Co-authored-by: akukalev <akukalev@gmail.com> Co-authored-by: Thomas Sparks <Thomas.Sparks@mdc-berlin.de>

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Rob Beagrie

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Merge branch 'v2.0.0-dev' into threshold-by-coverage * v2.0.0-dev: Add option to use NPMI normalisation (#24) Add fixed threshold option to process_nps command (#9) Fix issue with time.clock (#34) Cython packaging (#35)

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Rob Beagrie

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Add option to use NPMI normalisation (#24) * scripts for npmi normalization, saturaction curves and new reads-coverage calculations Separated NPMI script * Added npmi as an option for matrix normalisation Co-authored-by: Alexander Kukalev <akukalev@gmail.com> Co-authored-by: Thomas Sparks <Thomas.Sparks@mdc-berlin.de> * Added tests for NPMI * Updated documentation * Bump version number * Fix problem with deprecated time.clock() function * Rely on pandas for matrix compression * Bump version number * Added contributors file Co-authored-by: akukalev <akukalev@gmail.com> Co-authored-by: Thomas Sparks <Thomas.Sparks@mdc-berlin.de>

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PR merged pombo-lab/gamtools

Add option to use NPMI normalisation
+312 -60

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Rob Beagrie

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Cython packaging (#35) * Distribute compiled .c extensions not .pyx source * Pre-install cython on travis * Don't warn about f-string usage * Fix pylint errors and bump version

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Rob Beagrie

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Fix issue with time.clock (#34) * Fix issue with time.clock * Switch from coveralls to codecov on travis

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Merge branch 'v2.0.0-dev' into npmi-norm * v2.0.0-dev: Fix issue with time.clock (#34) Cython packaging (#35)

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Add fixed threshold option to process_nps command (#9) * Test for numpy handling boolean lists differently * Use boolean array not boolean list in filter_data

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Make submodules available using just 'import gamtools'

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Fix new pylint warnings

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Test numpy array emptiness more explicitly.

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Added functions to extract sub-regions of a matrix

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Merge pull request #11 from pombo-lab/gamtools_members Gamtools members

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Bump version number

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Merge pull request #12 from pombo-lab/submatrix_loc_string Submatrix loc string

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Merge pull request #13 from pombo-lab/v1.1.0-dev V1.1.0 changes

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Bump version number

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Check that pandas hasn't mangled numeric sample names

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Fixed pylint errors

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PR merged pombo-lab/gamtools

Fix issue with time.clock
+7 -6

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Fix issue with time.clock (#34) * Fix issue with time.clock * Switch from coveralls to codecov on travis

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Cython packaging (#35) * Distribute compiled .c extensions not .pyx source * Pre-install cython on travis * Don't warn about f-string usage * Fix pylint errors and bump version

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Merge branch 'v2.0.0-dev' into time_clock_fix * v2.0.0-dev: Cython packaging (#35)

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PR merged pombo-lab/gamtools

Cython packaging

Distribute compiled .c extensions rather than .pyx source

+40 -9854

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Cython packaging (#35) * Distribute compiled .c extensions not .pyx source * Pre-install cython on travis * Don't warn about f-string usage * Fix pylint errors and bump version

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Don't warn about f-string usage

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Fix pylint errors and bump version

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