Pinned Repositories
gdc_bam_library_exomekit_docker
Melanomas-ImmuneResistance-2019
This resource provides the code developed in the study of Jerby-Arnon _et al. "Single-cell RNA-seq of melanoma ecosystems reveals sources of T cell exclusion linked to immunotherapy clinical outcomes".
microbiome_helper
A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.
scOh
Single Cell Atlas - PDAC
Single-cell-multi-omic-profiling-of-glioblastoma-associated-myeloid-cells
Single-cell multi-omic profiling of glioblastoma-associated myeloid cells
merckey's Repositories
merckey/2019_scWorkshop
Repo for Physalia course Analysis of Single Cell RNA-Seq data
merckey/cellassign-paper
Analysis pipelines for cellassign manuscript
merckey/CNVworkflow_Terra_WDL
CNV analysis workflows for Terra workspace
merckey/colonicepithelium
merckey/docker-dropbox-app
:whale: A docker container for dropbox by App
merckey/facets_snakemake
Pipeline for running the FACETS copy number caller using Snakemake
merckey/gatk4-pathseq
This repo is archived, the these workflows are still available in the GATK repository under the scripts directory. The workflows are also organized in Dockstore in the GATK Best Practices Workflows collection.
merckey/gdc_qc_analysis
Somatic mutation pipeline comparison of TCGA samples between Genomic Data Commons (GDC) and MC3
merckey/Hera-T-Benchmark
Hera-T benchmark code
merckey/ISOWN
merckey/ITH_TCGA
merckey/KrumlovSingleCellWorkshop2020
Course Website
merckey/Lung-Development
merckey/Martire-et-al-2019-Nature-Genetics
Contains code for all the figures used in the paper
merckey/mc3_icgc_variant_pipeline
Variant analysis pipeline to compare the public PCAWG and MC3 mutation files generated by ICGC and TCGA
merckey/merckey.github.io
merckey/metaITH
A Tool for Analyzing Intratumor Heterogeneity at Multiple Levels
merckey/neusomatic
NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection
merckey/pdfs
Technically-oriented PDF Collection (Papers, Specs, Decks, Manuals, etc)
merckey/PeakCalling
Benchmarking ChIP-seq peak callers
merckey/picard
A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
merckey/RNA-seq-analysis
RNAseq analysis notes from Ming Tang
merckey/RNASeq_pipeline
merckey/scRNAseq_Benchmark
Bench-marking classification tools for scRNA-seq data
merckey/sepsis_signature
merckey/SGZ
merckey/tcga
Microbial analysis in TCGA data
merckey/tcga_mc3_pipeline
Pipeline developed to analyze intratumor heterogeneity. Uses TCGA MC3 data.
merckey/TOBI
TOBI predicts somatic variants from .vcf or .bam input
merckey/Workflows
Snakemake workflows for best practice genomic analysis