Projects in Awesome Lists tagged with biomedical-data-science

https://github.com/lengerichlab/compbiodatasetsformachinelearning

A Curated List of Computational Biology Datasets Suitable for Machine Learning

biomedical-data-science computational-biology computational-biology-datasets curated-list dataset datasets machine-learning

Last synced: 25 Feb 2025

https://github.com/epigen/atacseq_pipeline

Ultimate ATAC-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

atac-seq bash bioinformatics biomedical-data-science ngs pipeline python snakemake workflow

Last synced: 15 Apr 2025

https://github.com/borgwardtlab/s3m

A software package for statistically significant shapelet mining

biomedical biomedical-data-science shapelets significant-pattern-mining time-series time-series-analysis time-series-analysis-tool

Last synced: 21 Nov 2024

https://github.com/epigen/enrichment_analysis

A Snakemake workflow and MrBiomics module for performing genomic region set and gene set enrichment analyses using LOLA, GREAT, GSEApy, pycisTarget and RcisTarget.

atac-seq bioinformatics biomedical-data-science chip-seq enrichment-analysis gene-set-enrichment gene-sets genomic-regions motif-enrichment-analysis pipeline rna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/dea_limma

A Snakemake workflow and MrBiomics module for performing and visualizing differential (expression) analyses (DEA) on NGS data powered by the R package limma.

atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow

Last synced: 15 Apr 2025

https://github.com/epigen/scrnaseq_processing_seurat

A Snakemake workflow and MrBiomics module for processing and visualizing (multimodal) sc/snRNA-seq data generated with 10X Genomics Kits or in the MTX matrix file format powered by the R package Seurat.

10xgenomics bioinformatics biomedical-data-science cite-seq sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/genome_tracks

A Snakemake workflow and MrBiomics module for easy visualization of genome browser tracks of aligned BAM files (e.g., RNA-seq, ATAC-seq, scRNA-seq, ...) powered by the wrapper gtracks for the package pyGenomeTracks, and IGV-reports.

atac-seq bioinformatics biomedical-data-science genome-browser genome-track genomic-regions pipeline python rna-seq scrna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/epigen/dea_seurat

A Snakemake workflow and MrBiomics module for performing differential expression analyses (DEA) on (multimodal) sc/snRNA-seq data powered by the R package Seurat.

bioinformatics biomedical-data-science differential-expression-analysis scrna-seq single-cell snakemake snrna-seq visualization volcano-plot workflow

Last synced: 15 Apr 2025

https://github.com/epigen/mixscape_seurat

A Snakemake workflow and MrBiomics module for performing perturbation analyses of pooled (multimodal) CRISPR screens with sc/snRNA-seq read-out (scCRISPR-seq) powered by the R package Seurat's method Mixscape.

bioinformatics biomedical-data-science perturbation-analysis sccrispr-seq scrna-seq single-cell snakemake snrna-seq visualization workflow

Last synced: 15 Apr 2025

https://github.com/anthonymrios/adversarial-relation-classification

Unsupervised domain adaptation method for relation extraction

bioinformatics biomedical-data-science machine-learning natural-language-processing nlp nlp-machine-learning relation-extraction

Last synced: 20 Nov 2024

https://github.com/AnthonyMRios/adversarial-relation-classification

Unsupervised domain adaptation method for relation extraction

bioinformatics biomedical-data-science machine-learning natural-language-processing nlp nlp-machine-learning relation-extraction

Last synced: 09 May 2025

https://github.com/epigen/spilterlize_integrate

A Snakemake workflow and MrBiomics module to split, filter, normalize, integrate and select highly variable features of count matrices resulting from next-generation sequencing (NGS) experiments (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including confounding factor analysis and diagnostic visualizations.

atac-seq batch-effect bioinformatics biomedical-data-science chip-seq confounding-effects count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow

Last synced: 15 Apr 2025

https://github.com/hms-dbmi/EHRtemporalVariability

R package for delineating temporal dataset shifts in Eletronic Health Records

biomedical-data-science biomedical-informatics data-quality data-quality-monitoring dataset-shifts electronic-health-records time variability visualization

Last synced: 15 May 2025

https://github.com/a-r-j/drugtranslator

R package for translating between drug identifiers using the Chemical Translation Service (CTS)

biomedical-data-science biomedical-informatics chemical chemical-identifiers chemical-translation-service cheminformatics chemistry drug-development drug-discovery drug-repurposing identifiers r r-package

Last synced: 15 Apr 2025

https://github.com/robert-haas/kgw

Knowledge graph workflows with Python.

biomedical-data-science biomedical-knowledge-graph knowledge-graph knowledge-graph-construction

Last synced: 08 Mar 2025

https://github.com/arturomoncadatorres/breathing-rate-rsa

Implementation of the methods used to calculate (average) respiratory rate from heart rate variability as shown in the paper by Schafer and Kratky (2008).

biomedical-data-science biomedical-engineering breathing-rate ecg ecg-signal respiratory-rate signal-processing wearables

Last synced: 17 Feb 2025

https://github.com/scdamaddio/waltlabtools

A collection of tools for biomedical research assay analysis in Python.

assay biomedical-data-science calibration-curve concentrations curve-fitting diagnostics elisa modeling numpy python

Last synced: 13 Apr 2025

https://github.com/epigen/rnaseq_pipeline

RNA-seq Data Processing, Quantification and Annotation Snakemake Workflow and MrBiomics Module.

bash bioinformatics biomedical-data-science ngs pipeline python rna-seq rna-seq-pipeline rnaseq snakemake workflow

Last synced: 06 Apr 2025

https://github.com/carpentries-incubator/fair-for-busy-biologists

A short course on FAIR and data managment for biomedical research

alpha biomedical biomedical-data-science carpentries-incubator data-management english fair lesson

Last synced: 19 Feb 2025

https://github.com/maayanlab/genesetcart

GeneSetCart is an interactive web-based platform that enables investigators to gather gene sets from various sources; augment these sets with gene-gene co-expression correlations and protein-protein interactions; perform set operations on these sets such as union, consensus, and intersection; and visualize and analyze these gene sets.

biomedical-data-science biomedical-informatics geneset-enrichment geneset-enrichment-analysis genesets genomics proteomics proteomics-data-analysis transcriptomics

Last synced: 15 Mar 2025

https://github.com/sskender/biomedical-image-analysis

Biomedical Image Analysis FER

asub biomedical-data-science biomedical-image-processing cnn cnn-classification cnn-keras cnn-model pneumonia-classification pneumonia-detection vgg16 vgg16-model

Last synced: 22 Mar 2025

https://github.com/javadr/r-test

The solutions to two biomedical problems including finding "the list of differentially expressed genes" and "the 3 most frequently mutated genes in liver cancer"

biomedical-data-science

Last synced: 04 Mar 2025