shlienlab

All

11 repositories

otter-api-wrapper-python
Public
Python API wrapper for using the Otter webapp: otter.ccm.sickkids.ca
Python
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Other
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
otter-api-wrapper-R
Public
R API wrapper for using the Otter webapp: otter.ccm.sickkids.ca
R
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Other
•0•0•0•0•Updated Oct 28, 2024Oct 28, 2024
pre-otter
Public
RNA-seq pipeline to go from paired end fastq.gz files to TPM file and submit to the otter web app.
Python
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GNU Affero General Public License v3.0
•0•0•0•0•Updated Oct 24, 2024Oct 24, 2024
raccoon
Public
Multi-scale clustering in Python
optimization dimensionality-reduction differential-evolution knn umap hierarchical-clustering multi-scale scale-adaptive optimal-clusters clustering
Python
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GNU General Public License v3.0
•4•4•1•0•Updated Aug 10, 2022Aug 10, 2022
otter
Public
Ensemble of convolutional neural networks for transcriptional classification
rna-seq cancer tensorflow keras cnn gene-expression classification transcriptomics ensemble-classifier
Python
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Other
•2•0•1•0•Updated Aug 6, 2022Aug 6, 2022
RNAmp
Public
RNA Amplification in primary tumors
R
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Other
•0•1•0•0•Updated Aug 1, 2022Aug 1, 2022
WGS_somatic_pipeline
Public
A WDL workflow and wrapper for executing tumour + normal alignment, somatic small variant discovery, somatic structural variant and somatic copy number alteration discovery.
Perl
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GNU Affero General Public License v3.0
•1•3•0•0•Updated Jul 4, 2022Jul 4, 2022
SVetect
Public
A tool for identifying and classifying structural rearrangements and chromoplexy from high throughput sequencing data.
Python
•3•2•1•0•Updated Feb 12, 2018Feb 12, 2018
ShlienLab.Core.Filter
Public
A R package for filtering somatic mutation data used in the standard production pipeline in the Shlien Lab
R
•1•0•0•0•Updated May 18, 2017May 18, 2017
cosmic.cancer.gene.census
Public
A R package with common functions for annotating and filtering mutation data using the COSMIC cancer gene census
R
•1•1•0•0•Updated May 18, 2017May 18, 2017
ShlienLab.Core.SSM
Public
A R package for processing simple somatic mutations from MuTect2 data used in the Shlien Lab
R
•0•0•0•0•Updated May 18, 2017May 18, 2017