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cx-functional-analysis

cycif

Processing and analysys for Cyclic Immunofluorescence (CycIF) microscopy images

cyclicdominance

cystance

Generating model proteins optimised on geometry and accessibility of cysteine residues

cytosim

Cytosim is a cytoskeleton simulation engine

d2_nback_connectivity_elife2019

Data and code for the paper: 'Task-induced functional brain connectivity mediates the relationship between striatal D2/3 receptors and working memory', published in eLife 2019

damidseq_pipeline_output_dam-only_data

Pipeline to process DamID material and output Dam-only data files for profiling chromatin accessibility. This script is the pipeline generated by Owen Marshall (https://github.com/owenjm/damidseq_pipeline) with some minor modifications.

data-driven-analysis-lateralline

This repository hosts the code for "An Image-Based Data-Driven Analysis of Cellular Architecture in a Developing Tissue" (Hartmann et al., 2020).

data_analysis

datamanager

dataprocessdnaunzipping

Scripts for processing unzipping curves and hopping data. (collaboration with Bustamante group)

datasetdecay

Code relating to Dataset Decay article

dc-stats

Null Hypothesis Significance Testing by Randomization, Fieller's test and Effect size calculator, based on David Colquhoun's stats tools. GUIs for macOS, Win & Linux soon

debias

DeBias decouples global bias from direct interactions in co-orientation and co-localization data.

deepfly3d

Motion capture (markerless 3D pose estimation) pipeline and helper GUI for tethered Drosophila.

deepfreeze

CNN python pipeline for classifying freezing behavior + Matlab GUI for hand scoring freezing

deepfret-model

deepposekit

a toolkit for pose estimation using deep learning

deepposekit-data

Example datasets for DeepPoseKit

degradation_scripts

data analysis scripts for degradation pathway story

delay3ways

Our study on bridging the gap between animal & human studies of delay-discounting

demask

Deterministic Modeling for Analysis of complex Single molecule Kinetics --- MATLAB software for deterministic modeling and fitting with single molecule data

dendrite_fasciculation

dengue-antigenic-dynamics

Dengue antigenic variation and evolutionary dynamics

dengue_foi

Example code to estimate force of infection from age-stratified incidence data, as described in "Opportunities for improved surveillance and control of infectious diseases from age-specific case data: insight from dengue".

deploid

dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

deploid-data-benchmark-in_silico_field

deploid-data-benchmark-in_silico_lab_mixed_4s

deploid-utilities

detectionvsdiscrimination_fmri

fMRI project looking at the differences between perceptual detection and discrimination