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remove non-ascii characters
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Avsecz committed Dec 2, 2018
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2 changes: 1 addition & 1 deletion CpGenie/model-template.yaml
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Expand Up @@ -17,7 +17,7 @@ info:
github: krrome
name: CpGenie
version: 0.1
trained_on: "Samples from Chromosome 19 and 1422 were used for training, 1213 were used for hyper-parameter tuning and model selection, and the rest of the data were held-out for testing. In the analysis of variant-prediction, only meQTL and allele-specific methylation data from the held-out chromosome 10 and 11 were used. The 50 RRBS datasets of immortal cell lines, including GM12878, and the WGBS dataset of GM12878 were downloaded from ENCODE website (https://www.encodeproject.org/)."
trained_on: "Samples from Chromosome 1-9 and 14-22 were used for training, 12-13 were used for hyper-parameter tuning and model selection, and the rest of the data were held-out for testing. In the analysis of variant-prediction, only meQTL and allele-specific methylation data from the held-out chromosome 10 and 11 were used. The 50 RRBS datasets of immortal cell lines, including GM12878, and the WGBS dataset of GM12878 were downloaded from ENCODE website (https://www.encodeproject.org/)."
doc: >
Abstract:
DNA methylation plays a crucial role in the establishment of tissue-specific
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2 changes: 1 addition & 1 deletion DeepSEA/predict/model.yaml
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Expand Up @@ -31,7 +31,7 @@ info:
size and 4 nucleotides. Per sample, 919 probabilities of a
specific epigentic feature will be predicted.
cite_as: https://doi.org/10.1038/nmeth.3547
trained_on: "Chromosome 8 and 9 were excluded from training, and the rest of the autosomes were used for training and validation. 4,000 samples on chromosome 7 spanning the genomic coordinates 30,508,75135,296,850 were used as the validation set. Data were ENCODE and Roadmap Epigenomics chromatin profiles https://www.nature.com/articles/nmeth.3547#methods"
trained_on: "Chromosome 8 and 9 were excluded from training, and the rest of the autosomes were used for training and validation. 4,000 samples on chromosome 7 spanning the genomic coordinates 30,508,751-35,296,850 were used as the validation set. Data were ENCODE and Roadmap Epigenomics chromatin profiles https://www.nature.com/articles/nmeth.3547#methods"
training_procedure: https://www.nature.com/articles/nmeth.3547#methods
tags:
- Histone modification
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4 changes: 2 additions & 2 deletions DeepSEA/variantEffects/model.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -29,7 +29,7 @@ info:
size and 4 nucleotides. Per sample, 919 probabilities of a
specific epigentic feature will be predicted.
cite_as: https://doi.org/10.1038/nmeth.3547
trained_on: "Chromosome 8 and 9 were excluded from training, and the rest of the autosomes were used for training and validation. 4,000 samples on chromosome 7 spanning the genomic coordinates 30,508,75135,296,850 were used as the validation set. Data were ENCODE and Roadmap Epigenomics chromatin profiles https://www.nature.com/articles/nmeth.3547#methods"
trained_on: "Chromosome 8 and 9 were excluded from training, and the rest of the autosomes were used for training and validation. 4,000 samples on chromosome 7 spanning the genomic coordinates 30,508,751-35,296,850 were used as the validation set. Data were ENCODE and Roadmap Epigenomics chromatin profiles https://www.nature.com/articles/nmeth.3547#methods"
training_procedure: https://www.nature.com/articles/nmeth.3547#methods
tags:
- Histone modification
Expand Down Expand Up @@ -75,4 +75,4 @@ test:
expect:
url: https://s3.eu-central-1.amazonaws.com/kipoi-models/predictions/14f9bf4b49e21c7b31e8f6d6b9fc69ed88e25f43/DeepSEA/variantEffects/predictions.h5
md5: 365924f5d7f3372ef57721f2742192f9
precision_decimal: 6
precision_decimal: 6

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