amnahsiddiqa

CompMetabolomics

Docker_Singularity_HPC_Stuffs

mzkit

Data toolkits for processing NMR, MALDI MSI, MALDI single cell, LC-MS and GC-MS raw data, chemoinformatics data analysis and data visualization.

AnalyticalWorkflows

Scraps of my codes and hence of my life from here and there !

cloud_nfcore_pipelines

Tests for running nf-core pipelines on scale

datascience_jupyter_as

ImMSigDb

CloudThingies--SettingupSDKandFirebaseForProjects

RNASEQ_processing

SingleCellDataAnalysisResources

amnah-example-demo

TestAnalysis

amnahsiddiqa

Config files for my GitHub profile.

amnahsiddiqa.github.io

A beautiful, simple, clean, and responsive Jekyll theme for academics

awesome-compbio-chatgpt

An awesome repository of community-curated applications of ChatGPT and other LLMs im computational biology

cibersort_demonstration

For my personal use ;

fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

GeneAnnotations

MetaboAnnotation

High level functionality to support and simplify metabolomics data annotation.

metabolomics-ORA

Code for simulations in "Pathway analysis in metabolomics: Pitfalls and best practice for the use of Over-representation Analysis" Wieder C, Frainay C, Poupin N, Rodríguez-Mier P, Vinson F, et al. (2021) Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PLOS Computational Biology 17(9): e1009105.

Mouse-GEM

Genome-scale model for Mus musculus

mummichog

pathway and network analysis for metabolomics

pytorch-Deep-Learning

Deep Learning (with PyTorch)

reannotator-microarray-probes

resource_guide

Hagan Lab resources

RMISC_NOTEBOOKS

rnavar

gatk4 RNA variant calling pipeline

tcga-cancer-classification

A deep learning approach to classify cancer type from TCGA data.

testas

testQuarto

warpgroup

The warpgroup algorithm takes multiple LC/MS samples and determines: 1. Segregation of those peaks into compound groups; 2. Per-group consensus integration bounds; 3. Integration bounds for samples in which no peak was detected.

xcmsrocker

Rocker image for metabolomics data analysis