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advice

A repository of links with advice related to grad school applications, research, phd etc

als_genome_instability

Meta-analysis of ipsc-derived motor neurons in ALS

article-microarrays

Direct integration of microarray data — R scripts for comparing different microarray annotations and probesets selection for cross-platform direct data integration

auto-gpt

An experimental open-source attempt to make GPT-4 fully autonomous.

conor

R packages for cross-platform normalization of microarray data

dbnmicroarray

Classification for microarray data such as breast cancer, leukemia ALL-AML, lung cancer, colon tumor, and ovarian cancer using deep belief network algorithm.

disease-identification

Use Deep Learning Methods to analyze gene based microarray data to make classifcations on diseases, especially cancers, where the model is going to identify cancer stages for different cancers.

dwd

A python package implementing the distance weighted discrimination classifier

dwd-1

Distance Weighted Discrimination for Cross Platform Normalization - Python

dwd-2

Distance Weighted Discrimination performs statistical corrections to reduce systematic biases in microarray data sets.

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

feature-selection-for-machine-learning

Methods with examples for Feature Selection during Pre-processing in Machine Learning.

genomics

Scripts, utilities and programs for genomic bioinformatics.

hyperparameter-optimization-of-machine-learning-algorithms

Implementation of hyperparameter optimization/tuning methods for machine learning & deep learning models (easy&clear)

important-books-for-ml

incromap

Integrated analysis of Cross-platform MicroArray and Pathway data

learn-python

📚 Playground and cheatsheet for learning Python. Collection of Python scripts that are split by topics and contain code examples with explanations.

microarray-classification

DNA Microarray Gene Expression Data Classification Using SVM and MLP with Feature Selection Methods Relief and LASSO

ml_dl_microarrays

Here, we describe the comparison of the most used algorithms in classical ML and DL to classify carcinogenic tumors described on 11_tumor data base, obtaining accuracies between 76.97% and 100% for tumor identification. Our results bring up a more efficient an accurate classification method based on gene expression (microarray data) and ML/DL algor

orthogene

🧬 o r t h o g e n e 🧬✨✨✨✨✨✨✨ Interspecies gene mapping✨✨✨✨✨ 🦠 🔁 🌱 🔁 🌳 🔁 🍎 🔁 🍊 🔁 🪱 🔁 🪰 🔁 🐟 🔁 🦎 🔁 🐓 🔁 🦇 🔁 🐄 🔁 🐖 🔁 🐐 🔁 🐎 🔁 🐈 🔁 🐕 🔁 🐁 🔁 🐒 🔁 🦧 🔁 🦍 🔁 🏃‍♀️

probemapper-r

The R package client for ProbeMapper

pycombat

pyComBat is a Python 3 implementation of ComBat, one of the most widely used tool for correcting technical biases, called batch effects, in microarray expression data.

r-affymetrix-integration-pipeline

A pipeline for Affymetix microarray expression data integration with an example on itegrating 4 GEO datasets on first and second trimester human placenta.

rl-gensvm

Feature selection and tumor classification for microarray data using relaxed Lasso and generalized multi-class support vector machine

rnamethylation

rnaseq_titration_results

Cross-platform normalization enables machine learning model training on microarray and RNA-seq data simultaneously

scientific-visualization-book

An open access book on scientific visualization using python and matplotlib

scvi-tools

Deep probabilistic analysis of single-cell omics data

shap

A game theoretic approach to explain the output of any machine learning model.

statannot

add statistical annotations (pvalue significance) on an existing boxplot generated by seaborn boxplot