pjotrp (Pjotr Prins)

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Name: Pjotr Prins

Email

Company: Wageningen University

Location: Wageningen

Member Since: Jun 12, 2008 (about 1 year)

26 public repos
10 followers

Following 1 githubber and watching 41 repositories view all →

Public Repositories (26)

- 3
- 1
rqtl-mqm

R/QTL with MQM support

Last updated Fri Dec 11 06:56:42 -0800 2009
- 2
- 1
bigbio

Big data bioinformatics repository

Last updated Thu Dec 10 08:41:40 -0800 2009
- 14
- 6
biolib

BioLib brings together a set of opensource libraries written in C/C++ and makes them available fo...

Last updated Mon Dec 07 00:51:53 -0800 2009
- 2
- 1
cmake-support

CMake scripts for BioLib and ASciLib

Last updated Sat Dec 05 05:49:35 -0800 2009
- 1
- 1
EMBOSS

Git import of EMBOSS CVS repository for Biolib

Last updated Mon Nov 30 03:44:08 -0800 2009
- 1
- 26
bioruby

Central testing repository for the Bioruby project

Forked from bioruby/bioruby Sun Jul 20 09:09:02 -0700 2008

Last updated Thu Nov 26 03:42:16 -0800 2009
- 1
- 1
qnormalization

A library of parallel methods for gene-expression Q-normalization

Forked from ots/qnormalization Wed Jul 08 23:21:45 -0700 2009

Last updated Wed Nov 11 05:12:13 -0800 2009
- 1
- 0
genfrag

TDF predictor - copy of Rubyforge site

Last updated Wed Aug 19 23:12:36 -0700 2009
- 1
- 1
biopp-numcalc

Bio++ numcalc module

Last updated Mon Aug 17 02:06:25 -0700 2009
- 1
- 1
biopp-phyllib

Last updated Mon Aug 17 02:04:11 -0700 2009
- 1
- 1
biopp-popgenlib

Bio++ popgenlib module

Last updated Mon Aug 17 02:02:55 -0700 2009
- 1
- 1
biopp-seqlib

Bio++ seqlib module

Last updated Mon Aug 17 02:02:13 -0700 2009
- 1
- 1
biopp-utils

Bio++ utils module

Last updated Mon Aug 17 01:57:00 -0700 2009
- 2
- 2
libsequence

The libsequence library (for BioLib)

Last updated Tue Aug 04 05:28:13 -0700 2009
- 4
- 1
rqtl

R/qtl mapping software

Last updated Tue Jul 21 07:03:46 -0700 2009
- 1
- 4
math--gsl

Perl interface to the GNU Scientific Library

Forked from leto/math--gsl Sat Apr 04 02:49:14 -0700 2009

Last updated Sat May 23 02:13:15 -0700 2009
- 2
- 1
ascilib

A science library - SWIG mappings

Last updated Sat May 23 01:02:10 -0700 2009
- 2
- 2
biopp

A reference repository of the Bio++ project (no history)

Last updated Fri May 22 03:15:01 -0700 2009
- 1
- 1
bio---numcalc

Trial repository for numcalc

Last updated Fri May 22 03:03:26 -0700 2009
- 1
- 0
qnorm

High performance quantile normalization (for BioLib)

Last updated Sat May 09 05:32:42 -0700 2009
- 2
- 1
swigdoc

SWIG XML document generator

Last updated Sat Apr 25 02:05:34 -0700 2009
- 1
- 0
biotools

A set of tools and filters

Last updated Sat Mar 21 03:15:06 -0700 2009
- 0
- 0
bioruby-support

Supporting files and scripts for the Bioruby project

Last updated Thu Mar 12 09:23:16 -0700 2009
- 1
- 6
rubydoctest

Ruby version of Python's doctest tool, but a bit different

Forked from tablatom/rubydoctest Fri Mar 06 06:51:57 -0800 2009

Last updated Fri Mar 06 06:54:25 -0800 2009
- 1
- 0
bionix

Bio packages for the Nix package system

Last updated Tue Oct 07 08:06:57 -0700 2008
- 1
- 1
biopp-submodules

Bio++ master mirror of CVS repository

Created Mon Aug 17 01:54:59 -0700 2009

Public Activity

pjotrp pushed to master at pjotrp/rqtl-mqm Fri Dec 11 06:56:42 -0800 2009

HEAD is c6fc5e68b396de9d5e334dbbcbd1dd25d1b5a2dc

2 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 06:56:13 -0800 2009

HEAD is c6fc5e68b396de9d5e334dbbcbd1dd25d1b5a2dc

pjotrp committed c6fc5e68:

Modified MQM-TODO

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 06:24:57 -0800 2009

HEAD is b62b620fcbe281f60fec137b69c476bf45b7f795

pjotrp committed b62b620f:

mqmaugment: aligned parameter list for easier reading

pjotrp pushed to master at pjotrp/rqtl-mqm Fri Dec 11 06:14:19 -0800 2009

HEAD is 74cc3b5b2958a5cac51e26be2f6a657812321785

56 commits »

DannyArends committed 4f7559cc:

Output shouldn't show Neglect it should show minprob
DannyArends committed 88420154:

MQMaugment updates
DannyArends committed 7d45aad4:

minprob=1 so we never drop individuals when we call mqmaugment(cross) without parameters.
DannyArends committed 233c8b7c:

Neglect -> minprob inside C
DannyArends committed 76117b31:

Name of mqmaugment function changed in C
DannyArends committed 13470de9:

Regression in GIT showed no sign of dropping of markers
pjotrp committed ddfa28c1:

MQM augmentation: shared text gets included from one source (experimental)
pjotrp committed fc3f9e8a:

MQM augmentation: adding to tutorial and documentation
pjotrp committed b0ebdca1:

scanone_mr gets forced C linkage
pjotrp committed d0f8310c:

R/qtl: changed build order of CMake macros
pjotrp committed b0189a85:

Biolib: aligned CMakeLists.txt with the newer Biolib build scripts
pjotrp committed 7cdb18c6:

Regression test: set minprob to 1
pjotrp committed 550ee064:

Regression test changed because we use mintest=0.1, rather than 1.0
pjotrp committed 1e62a34c:

Removing generated document files
pjotrp committed 034760b0:

mqmaugment: renamed augmetnt_aboveprob parameter to minprob
pjotrp committed 937932cf:

mqmaugment: changed descriptions
pjotrp committed 047d0fc2:

Docs: mqmaugment description
pjotrp committed 92cd9946:

All tests pass after removing the neglect=1 parameter
pjotrp committed 183e14d2:

Updated regression output
pjotrp committed 3eb0b7ad:

Removed sign-warnings of mqmmain.cpp

And 36 more commits...

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 06:09:58 -0800 2009

HEAD is 74cc3b5b2958a5cac51e26be2f6a657812321785

pjotrp committed 74cc3b5b:

Renamed TODO file for MQM

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 06:07:39 -0800 2009

HEAD is e7ec9af2bbe08c6b04480116a4b1593f271314fe

7 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 02:05:54 -0800 2009

HEAD is 454c4ddc4dcbb6336e6992d0991607eda6ad56f4

pjotrp committed 454c4ddc:

man: MQM.Rd uses shared example

pjotrp pushed to danny at pjotrp/rqtl-mqm Fri Dec 11 02:00:41 -0800 2009

HEAD is f13d6c9dd7b3eedbbd6176bb62bb44754bc1f612

6 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Fri Dec 11 02:00:39 -0800 2009

HEAD is 11ecc3544c5fcb05b2d00fc27d902d5dab43a792

10 commits »

pjotrp committed 11ecc354:

man: mqmaugment uses shared info
pjotrp committed 58d85d72:

mqmaugment: Modifying textual information
DannyArends committed ca192476:

Zoom to 3 chromosomes which look pretyt
DannyArends committed f6865b92:

Lets hope the difference shows between the plots now
DannyArends committed c998265f:

plots, removed a bug where chromosomes would be considered factors and no line would be plotted
DannyArends committed c93e862e:

Sweave again
DannyArends committed 4e072315:

Minor updates removed an empty page
DannyArends committed 135a3c6e:

Updates mqmscan text, somewhat more precize and more scientific (i hope)
DannyArends committed 574a19e2:

Latex errors
DannyArends committed a65a3a43:

Added todolist for MQM

pjotrp pushed to ORF at pjotrp/bigbio Thu Dec 10 08:41:40 -0800 2009

HEAD is 9576664bb614d3a95a4e1f27e47f4f0a758d93b7

2 commits »

pjotrp pushed to ORF at pjotrp/bigbio Thu Dec 10 04:58:46 -0800 2009

HEAD is cf90539ff60885e24d9fe5de522c7a54dfd162bb

2 commits »

pjotrp pushed to master at pjotrp/bigbio Thu Dec 10 04:56:03 -0800 2009

HEAD is fdf675fbe8e3b22a74841ee6a7fe2b6741b3531b

pjotrp committed fdf675fb:

Add example for NT2AA translation in 6 frames using EMBOSS

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Wed Dec 09 07:12:16 -0800 2009

HEAD is 6a57305253b068b754c683770329b69d6e69efcb

3 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Wed Dec 09 07:08:15 -0800 2009

HEAD is 40d90f4d01e272022486f6b01b72cfdf0f01d82e

2 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Wed Dec 09 06:38:18 -0800 2009

HEAD is 9fd4c0cbbf8e73776910af352f000a6361ac2afd

8 commits »

pjotrp committed 9fd4c0cb:

repl_inputs: added \mqmauthors macro
pjotrp committed 5e1b62a6:

repl_inputs: add keywords
pjotrp committed 28a200ed:

repl script: make certain a file is closed before reopening for writing
pjotrp committed 1fe339bd:

Script for replacing content of Rd files with shared text
pjotrp committed d046683c:

limitations.txt: removed LaTeX
pjotrp committed 38e3694c:

Rename shared file
pjotrp committed 76e7824f:

MQM.Rd: clean up
pjotrp committed 890150c1:

rd does not care for the LaTeX \input command

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Wed Dec 09 01:06:47 -0800 2009

HEAD is 14b4b7c9992b49db9dc25c6f30d4e3bcdba8695b

10 commits »

pjotrp committed 14b4b7c9:

chapter12: a few notes
pjotrp committed b5884347:

mqmaugment: having a second look at the logic of minprob/neglect -
DannyArends committed 0d262047:

Neglect in output changed to Minprob S)
DannyArends committed f354d07d:

In standalone its now also minprob (no more neglect xcept internally)
DannyArends committed 4f7559cc:

Output shouldn't show Neglect it should show minprob
DannyArends committed 88420154:

MQMaugment updates
DannyArends committed 7d45aad4:

minprob=1 so we never drop individuals when we call mqmaugment(cross) without parameters.
DannyArends committed 233c8b7c:

Neglect -> minprob inside C
DannyArends committed 76117b31:

Name of mqmaugment function changed in C
DannyArends committed 13470de9:

Regression in GIT showed no sign of dropping of markers

pjotrp pushed to rqtl at pjotrp/biolib Mon Dec 07 00:51:54 -0800 2009

HEAD is 2755ff1e5fa52dca788efc2382b9689d2510441c

5 commits »

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Mon Dec 07 00:51:35 -0800 2009

HEAD is ddfa28c1ec6f5417f5c1f1647327c9805a17512d

4 commits »

pjotrp pushed to master at pjotrp/cmake-support Sat Dec 05 05:49:35 -0800 2009

HEAD is 61b3bb9d9bc5258814f47c6e408ecf084dcb3358

3 commits »

pjotrp pushed to rqtl at pjotrp/biolib Sat Dec 05 05:49:26 -0800 2009

HEAD is 48a89d67cdee28ecc6cb3cec573daf656dabd896

98 commits »

diavy committed 3aa7e083:

add libsequence to src/mappings/swig/python/CMakeLists.txt
diavy committed 1321d940:

Merge branch 'libsequence'
diavy committed 1641e42b:

add libsequence to src/mappings/swig/python/CMakeLists.txt
diavy committed a55e939b:

modified: src/mappings/swig/python/CMakeLists.txt
diavy committed e0b4c2f9:

modified: src/mappings/swig/python/CMakeLists.txt
diavy committed 455e5d01:

modified cmake-support
diavy committed 4da5f458:

Modified src/mappings/swig/python/CMakeLists.txt
pjotrp committed c72f1083:

Updated cmake-support
pjotrp committed 357209de:

Merge branch 'release_candidate' of git@github.com:pjotrp/biolib into libsequence
pjotrp committed e1d49638:

libsequence Python module compiles
pjotrp committed d1ba695b:

Merge branch 'master' of git://github.com/diavy/biolib into libsequence
pjotrp committed 1cf9326e:

Merge branch 'release_candidate' into libsequence
diavy committed 2664afde:

Merge branch 'libsequence'
diavy committed aa39c511:

Add Mac OS X support in FindMapModules.cmake and FindMapLibraies.cmake
diavy committed e31625e0:

built a dynamic library for General IO module in libsequence
diavy committed 8a5d2986:

Added 1)src/mappings/swig/libsequence.i
diavy committed d1b44e05:

1. built libsequece dynamic library for General IO module of libsequence:libbiolib_libsequence-0.0.4.dylib in ./src/clibs/libsequence/build
pjotrp committed 9738b6f9:

Building libsequence
pjotrp committed 6016100e:

Build system for libsequence
pjotrp committed c7ab0c9d:

Adding libsequence-1.6.6 as a submodule

And 78 more commits...

pjotrp pushed to pjotr at pjotrp/rqtl-mqm Sat Dec 05 04:37:51 -0800 2009

HEAD is b0189a853b3071271e4696498110ef6b3c1b0c1a

293 commits »

DannyArends committed 478c1510:

Working MQMstandalone using getopts and the new loading functions (dataaugmentation routine not fixed yet)
DannyArends committed 2b5898ba:

Values now returned, n passed on into analysef2, almost working with getopts
DannyArends committed cecf01a5:

cofactorfile for firsttestset, this came from the settingsfile, now commandline
DannyArends committed a53d8222:

opt_main into MQM, still need a way to return multiple arrays back to main from a function, it compiles,runs and fails as we dont get the positions back from the functions yet
DannyArends committed a43d9771:

New settingsfileformat (added number of markers)
DannyArends committed 66a37bd1:

Updates markerpositionfile to new format (including chromosomes)
DannyArends committed 6bff9f5a:

Added some extra comments
DannyArends committed 1e5ae2d5:

Some more additions to opt_main.cpp, reading setting,geno,pheno,markers -still untested-
DannyArends committed 64829b93:

New opt main, untested yet. getting closer to including in MQMmain
DannyArends committed 8cf27cd6:

opt_main.cpp: unsigned int argc
DannyArends committed 29dfd963:

opt_main.cpp: Added a fileextists check (includes <iostream> & <fstream>
DannyArends committed 90259f56:

Initial files from data(hyper) [r/qtl] suitable for MQM standalone analysis (untested yet)
DannyArends committed 100630d9:

Forgot minor updates, printing Switches when error occured.
DannyArends committed 7aa5fb9b:

opt_main.cpp updated to new version in master
pjotrp committed d9aaaf21:

Formatting
pjotrp committed 14f3a561:

Merge branch 'master' of git://github.com/DannyArends/rqtl-mqm into danny
DannyArends committed d561ac7e:

opt_main.cpp for options to MQM using getopt. Exits when needed options are not present (basic return)
kbroman committed fa25bf72:

Add example on reading files from web in help file for read.cross.
kbroman committed 87e74c38:

Change version number and date.
kbroman committed cfdc8a46:

Add item to TODO list.