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[datasets] added singlecell dataset

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Max Zwiessele 2014-05-09 14:05:57 +01:00
parent 675d498794
commit a717c03866
3 changed files with 22 additions and 410 deletions
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410
GPy/util/data_resources.json
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File diff suppressed because one or more lines are too long

14
GPy/util/datasets.py
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@ -717,7 +717,19 @@ def hapmap3(data_set='hapmap3'):
inandf=inandf,
populations=populations)
return hapmap
def singlecell(data_set='singlecell'):
if not data_available(data_set):
download_data(data_set)
dirpath = os.path.join(data_path, data_set)
data = np.loadtxt(os.path.join(dirpath, 'singlecell.csv'), delimiter=",", dtype=str)
genes = data[0, 1:]
labels = data[1:, 0]
Y = np.array(data[1:, 1:], dtype=float)
return data_details_return({'Y': Y, 'info' : "qPCR Singlecell experiment in Mouse, measuring 48 gene expressions in 1-64 cell states. The labels have been created as in Guo et al. [2010]",
'genes':genes, 'labels':labels,
}, data_set)
def swiss_roll_1000():
return swiss_roll(num_samples=1000)

8
GPy/util/datasets/data_resources_create.py
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@ -161,6 +161,14 @@ data_resources = {'ankur_pose_data' : {'urls' : [neil_url + 'ankur_pose_data/'],
'citation': """Gibbs, Richard A., et al. "The international HapMap project." Nature 426.6968 (2003): 789-796.""",
'license' : """International HapMap Project Public Access License (http://hapmap.ncbi.nlm.nih.gov/cgi-perl/registration#licence)""",
'size' : 2*1729092237 + 62265},
'singlecell' : {'urls' : ["http://staffwww.dcs.sheffield.ac.uk/people/M.Zwiessele/data/singlecell/"],
'files' : [['singlecell.csv']],
'details' : "qPCR Singlecell experiment in Mouse, measuring 48 gene expressions in 1-64 cell states. The labels have been created as in Guo et al. [2010]",
'citation' : "Guoji Guo, Mikael Huss, Guo Qing Tong, Chaoyang Wang, Li Li Sun, Neil D. Clarke, Paul Robson, Resolution of Cell Fate Decisions Revealed by Single-Cell Gene Expression Analysis from Zygote to Blastocyst, Developmental Cell, Volume 18, Issue 4, 20 April 2010, Pages 675-685, ISSN 1534-5807, http://dx.doi.org/10.1016/j.devcel.2010.02.012. (http://www.sciencedirect.com/science/article/pii/S1534580710001103) Keywords: DEVBIO",
'license' : "ScienceDirect: http://www.elsevier.com/locate/termsandconditions?utm_source=sciencedirect&utm_medium=link&utm_campaign=terms",
'size' : 233.1,
}
}
with open('data_resources.json', 'w') as f: