collaborativebioinformatics/Biobank_notebooks collaborativebioinformatics/Biobank_notebooks

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  • Created over 3 years ago
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collaborativebioinformatics/Biobank_notebooks
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collaborativebioinformatics

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Repository Details

Notebooks for working with Biobank level data

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1

STRdust

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2

GeneVar

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3

Sniphles

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4

nibSV

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5

Disease_subsetting

Colorectal cancer CMs subtyping and personalized medication recommendation based on RNA seq pathway analysis
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6

GeneVar2

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7

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8

omics_clinical_reporting

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9

kvar

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10

PhytoKmerCNV

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11

clinical_SVs

Clinically reportable structural variant calls
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12

PRS_reporting

Clinical Reporting of Polygenic Risk Scores
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13

SVHack_Mendelian

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14

Viewing_expressed_variants

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15

Disease_Subtyping_2022

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16

INSeption

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17

snpReportR

Develop a tool to facilitate genetic reporting of expressed variants
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18

CNV2SV

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19

RPG_Pikachu

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20

CleanSV

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21

omics_to_omop

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22

RNAseq_Dashboard

A dashboard for comparison of RNAseq approaches
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23

coronasv

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24

swagg

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25

SVeedy

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26

Genevar22

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27

cov2db

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28

CRC-Dashboard

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29

vcfs2kgs

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30

GrOMOP

Genome Graphs into OMOPOMICs
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31

Differential_Expression_and_Variant_Association

aka Environmental effects on risk variants
Jupyter Notebook
2
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32

genome_and_knowledge_graphs

Genome and Knowledge Graph Theory
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33

kTom

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34

virussusceptibility

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35

graphbasedtuning

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36

SVHack_metagenomics

Everything is bigger in Texas: Pan-Structural Variation hackathon in the Cloud!
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37

isocomp

Isocomp provides tools to compare any number of transcriptome assemblies (GTF + fasta) from long read RNAseq
HTML
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38

kgbasedvalidation

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39

SVHack_Pangenomics

2
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40

SVHack_assemblyvmapping

2
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41

starfishDiscovery

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1
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42

Data_Integration_CoVID

Omopomics-style data integration for HLA, RNAseq and virus sequences
1
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43

The_X_team

Assembly based validation tool.
Python
1
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44

NIST-GREX

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1
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45

beautifulsoup

Web scraping and yes, actual soup recipes
1
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46

tandemrepeats

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1
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47

CI4CCREFS

Data Management for Transformer Models -- References
1
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48

VariantSurvival

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1
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49

SVHack_HG002Mosaic

1
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50

Disease_subtyping_knowledge_graph

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51

PanOriginSV

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52

DSVifier

A bioinformatics pipeline for rapidly evaluating variants and identifying causal variants.
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53

expression_and_SNPs_to_clinic

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1
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54

TCRs_to_clinic

Clinically Reportable TCR repertoires
1
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55

deeplearningmetagenomics

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56

imavirus

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