eLife Sciences's Projects
Divergent Virus & Mobile Element Genome Annotation Pipeline
Analysis and modeling code for "Receptive field center-surround interactions mediate context-dependent spatial contrast encoding in the retina"
Code used for figure generation and statistical analysis for https://www.biorxiv.org/content/10.1101/552117v2
Github repository for cerebellum gradients project
MATLAB and R scripts to process microscopy image stacks for immuno stained oxytocin positive neurons
Program to fit chemical exchange induced shift and relaxation data
These scripts and files were used to re-analyize the Chen et al., 2018 manuscript titled "Single nucleus sequencing reveals evidence of inter-nucleus recombination in arbuscular mycorrhizal fungi"
Code for analysis of Aspergillus nidulans H3, H3K9ac and K3K14ac ChIP-Seq libraries
Data and code for Chittajallu et al., 2020 'Activity-dependent tuning of intrinsic excitability in mouse and human neurogliaform cells' https://www.biorxiv.org/content/10.1101/2020.03.24.004465v2
Pooled analysis of mortality and QRS widening in chloroquine self-poisoning patients and healthy volunteers: estimating safety of currently trialled chloroquine regimens
A manuscript on the protocol on chronic recording from Neuropixels probes
Neuropixels case for chronic recordings in freely moving mice.
An ImageJ plugin to quantify ciliary shape, length, and fluorescence.
Analysis pipelines to call and analyze transcript errors from CirSeq data
LFP recordings from a Long-Evans rat before and after closed-loop theta phase-locked stimulation.
Repo for description of Singapore and Tianjin COVID19 clusters, and related estimation
clathrin-mediated endocytosis analysis
CNApp represents the first web tool to perform a comprehensive and integrative analysis of copy number alterations (CNAs) in a user-friendly interface. The software uses segmented data from either aCGH, SNP-array, whole-exome sequencing or whole-genome sequencing to assess sample profiles and CNA levels, establishing associations with molecular and clinical features. CNApp has three main sections: Re-Seg & Score, Region profile and Classifier model
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Constrained Nonnegative Matrix Factorization for microEndoscopic data
Simulation and analysis code for Lindsay and Miller 2018
This software is used to determine viral scission time from CO2 dependent modulation in fluorescence intensity