const-ae/Multi-omics-Data-Integration-course

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Created 12 months ago
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const-ae/Multi-omics-Data-Integration-course

const-ae

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Temporary Repository for the EMBO 2024 Multi-Omics course

ggsignif

Easily add significance brackets to your ggplots

ggupset

Combination matrix axis for 'ggplot2' to create 'UpSet' plots

tidygenomics

Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

lemur

Latent Embedding Multivariate Regression

sparseMatrixStats

Implementation of the matrixStats API for sparse matrices

transformGamPoi-Paper

transformGamPoi

Variance stabilizing transformation for Gamma Poisson distributed data

proDA

Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/

mixdir

Cluster high dimensional categorical datasets

pyLemur

A Python implementation of the LEMUR algorithm for analyzing multi-condition single-cell RNA-seq data.

Jupyter Notebook

Neural_Network_DNA_Demo

Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

Jupyter Notebook

einsum

Einstein Summation for Arrays in R

CoefExplainer

Understand How to Interpret the Coefficients of a Categorical Linear Model

motif_plotter

A simple tool to create DNA motif plots based directly on matplotlib to enable construction of complex plots

Jupyter Notebook

CoronaDensity

ggquadrilateral

A quadrilateral geom for ggplot2

HighlyReplicatedRNASeq

Collection of Bulk RNA-Seq Experiments With Many Replicates

ggplot2_basics_to_extensions

Material from my talk "ggplot2: whistlestop tour from basics to extensions" at the Oxford R User group meetup.

gggroupedscale

Grouped Discrete Scale for 'ggplot2'

kmeansPoi

R package for K-means clustering of Counts

SkiingInSingapore

My solution for the coding challenge published by RedMart.

proDD

Differential Detection for Label-free (LFQ) Mass Spec Data

transformGamPoi-ShinyApp

Source code for the Shiny App of Comparison of Transformations for Single-Cell RNA-Seq Data

ggbezier

Bezier curves for 'ggplot2'

MyWorkflowManager

This is a simple self-written R workflow manager for slurm systems that I use to automate the submission of jobs

glmGamPoi-Paper