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awesome-bitcoin-cash

A curated list of awesome things related to Bitcoin Cash

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bio.jl

Bioinformatics and Computational Biology Infrastructure for Julia

bioservices

Access to Biological Web Services from Python.

clinstudyweb

This package was developed by Tim Rayner at the CIMR (Smith Lab) but has disappeared from CRAN/Bioconductor. Adding latest stable release to my page for anyone in the group to use.

dddmaps

Mutability adjusted proportion of singletons calculation using synonymous SNPs from the DDD unaffected parents.

dddnoncoding2017

Code for paper published in March, 2017 analysing the role of de novo mutations in severe developmental disorders (part of the deciphering developmental disorders project).

de_novo_noncoding

Description of R and Python code and other pipelines to test enrichment of de novo mutations in the DDD non-coding regions.

deeplift

Public facing deeplift repo

denovo_regs

denovosim

Simulate de novo mutations using model based on trinucleotide mutation rate model introduced in Samocha et. al, 2014. Users can condition on number of patients in a study, and number of mutations observed. Updates to the model planned and tracked in issues section.

denovotf

Calculating change in binding affinity for predicted TF binding sites as a result of de novo mutations in non-coding regions. Uses JASPAR database for TF binding prediction.

explore

fresh-dnm

gwc

Method for generating genome-wide constraint metrics comparing observed to expected variation. Expected is calculated using an updated mutation rate model with sequence context + 32 additional features.

lens

A novel way of seeing content

london_data_sci_pca_supervised

modelling_excess

mscentipede

A hierarchical multiscale model for inferring transcription factor binding from chromatin accessibility data.

mupit

De novo mutation recurrence significance testing

ncbi_data_scrape

use biopython entrez to pull useful data from ncbi (i.e. pubmed metadata)

pca_datascisummit

recessivestats

repository for analysis of recessive genes

repscan

Scan list of de novo mutations against input gappedPeak or broadPeak files from the Roadmap Epigenomics Project (REP). Focus of the code base here is the identification of de novo mutations in regulatory regions that are active in development. As such, data used in example scripts will be primarily adult or fetal brain histone marks and DNAse hypersensitivity.

rupit

Significance testing for recurrence of de novo regulatory mutations.

selection2

singletonmetric

smithlabarray

This package was developed by Tim Rayner at the CIMR (Smith Lab) but has disappeared from CRAN/Bioconductor. Adding latest stable release to my page for anyone in the group to use.

tachyon

High-level API for storing and querying sequence variant data