hermidalc
cancer data science / bioinformatics / computational biology / genomics
University of PittsburghPittsburgh, PA
Pinned Repositories
dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
perl-rna-seq-star
STAR + HTSeq + featureCounts RNA-seq processing pipeline environment and wrapper script, including SRA query, download, and caching functionality and useful reuse/restart features
rna-seq-star-gex
STAR + edgeR/DESeq2/limma-voom + GSEA RNA-seq gene expression analysis workflow
sklearn-bio-workflows
Framework to build, evaluate, select, and compare ML classification and regression models using high-dimensional biological data and other covariates
sksurv-bio-workflows
Framework to build, evaluate, select, and compare ML survival analysis models using high-dimensional biological data and other covariates
tcga-microbiome-prediction
Predictive models and analysis of cancer prognosis and drug response using primary tumor microbial abundances derived from WGS and RNA-seq sequencing data for 32 TCGA cancers (Poore et al. Nature 2020), including equivalent models using TCGA RNA-seq gene expression and combined microbial abundance and gene expression for comparison.
tcga-wgs-kraken-microbial-quant
Kraken2 + Bracken based pipeline for classifying and quantifying microbial reads from GDC TCGA WGS data
hermidalc's Repositories
hermidalc/sklearn-bio-workflows
Framework to build, evaluate, select, and compare ML classification and regression models using high-dimensional biological data and other covariates
hermidalc/perl-rna-seq-star
STAR + HTSeq + featureCounts RNA-seq processing pipeline environment and wrapper script, including SRA query, download, and caching functionality and useful reuse/restart features
hermidalc/agamemnon
Accurate metagenomic/metatranscriptomic analysis pipeline
hermidalc/cancer-mbiome-ict-net
Cancer microbiome immune checkpoint therapy network analysis
hermidalc/dragonfish
A fast, efficient, and accurate functional and taxonomic meta-omic profiler built on Pufferfish and the ccdBG
hermidalc/rna-seq-star-gex
STAR + edgeR/DESeq2/limma-voom + GSEA RNA-seq gene expression analysis workflow
hermidalc/sklearn-extensions
scikit-learn extensions
hermidalc/sksurv-bio-workflows
Framework to build, evaluate, select, and compare ML survival analysis models using high-dimensional biological data and other covariates
hermidalc/sksurv-extensions
scikit-survival extensions
hermidalc/confero
Confero Project Repository
hermidalc/feature-id-mapping
Feature ID Mapping Script Repository
hermidalc/fuzzy-kmer-seq-aligner
Fuzzy k-mer local sequence aligner inspired by Healy J, Chambers D. Approximate K-mer Matching Using Fuzzy Hash Maps (2014) though with many changes and enhancements
hermidalc/gp-sym-regr-bio
Genetic programming symbolic regression vs standard supervised machine learning methods for prediction in biological data
hermidalc/htslib
C library for high-throughput sequencing data formats
hermidalc/humann
HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
hermidalc/JAMS_BW
Just a Microbiology System (JAMS) - a suite for analyzing microbiological sequencing data for use on NIH HPC systems (Biowulf)
hermidalc/lifelines
Survival analysis in Python
hermidalc/ml-lung-cancer
ML prediction in lung cancer
hermidalc/ml-resp-cancer-mbiome
ML prediction of drug response in cancer using microbiome data
hermidalc/ml-resp-cancer-xcell-gex
ML prediction of drug response in cancer from xCell and gene expression data
hermidalc/nci-ctd2-dashboard-tmpl-helper
NCI CTD^2 Dashboard Template Helper
hermidalc/nci-ocg-dcc
NCI OCG DCC Repository
hermidalc/pufferfish
An efficient index for the colored, compacted, de Bruijn graph
hermidalc/rpy2-feedstock
A conda-smithy repository for rpy2.
hermidalc/scikit-feature
open-source feature selection repository in python (DMML Lab@ASU)
hermidalc/scikit-learn
scikit-learn: machine learning in Python
hermidalc/scikit-survival
Survival analysis built on top of scikit-learn
hermidalc/SeqLib
C++ htslib/bwa-mem/fermi interface for interrogating sequence data
hermidalc/snakemake-wrappers
Snakemake modular component wrappers for use in workflows
hermidalc/ssGSEA2.0
Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)