migbro
Bioinformatics Engineer, lead developer within BIXU team at the Center for Data Driven Discovery (D3b) at the Children's Hospital of Philadelphia (CHOP).
@d3b-center @kids-first
Pinned Repositories
alignment
DNAseq alignment pipelines for use on HPC systems.
alignment2
Will evolve to the new alignment pipeline to be run on cloud instead of cluster
beta-somatic-pipe
A dev version of somatic calling pipe used by cbttc for wgs and pnoc
bioconductor.org
Website for bioconductor.org
clustermap_tools
Somewhat specialized python scripts to create unsupervised hierarchical clustering heat maps
crispr_donor_pipe
echtvar
using all the bits for echt rapid variant annotation and filtering
kfdrc-toolbox
migbro's Repositories
migbro/kfdrc-toolbox
migbro/alignment
DNAseq alignment pipelines for use on HPC systems.
migbro/alignment2
Will evolve to the new alignment pipeline to be run on cloud instead of cluster
migbro/beta-somatic-pipe
A dev version of somatic calling pipe used by cbttc for wgs and pnoc
migbro/bioconductor.org
Website for bioconductor.org
migbro/clustermap_tools
Somewhat specialized python scripts to create unsupervised hierarchical clustering heat maps
migbro/crispr_donor_pipe
migbro/echtvar
using all the bits for echt rapid variant annotation and filtering
migbro/filter_read_by_var
migbro/hgac_lims
django site to serve seqConfig
migbro/IGSB_oxoG_tools
migbro/ipython_notebooks
Collection of notebooks, mostly useful only to me
migbro/kf-sentieon-workflows
Sentieon workflow for Kids-First
migbro/mouse_filter
Filter mouse reads from a Human PDX derived .bam
migbro/ngs_checkmate_wf
A cwl workflow to run ngs_checkmate on large datasets
migbro/OpenPBTA-manuscript
The manuscript repository for the Open Pediatric Brain Tumor Atlas Project
migbro/OpenPedCan-analysis
The analysis repository for the Open Pediatric Cancer Project
migbro/project-specific
Repo with project-specific scripts. Not likely useful to general public
migbro/RNAseq
RNAseq pipeline
migbro/salmon-rnaseq
scRNA-seq pipeline using Salmon for quantification
migbro/seqConfig
Sequencing configuration generator
migbro/snf_robustinator
migbro/swift_seq_utils
migbro/variant_viewer_update_tools
Plugin to upload variant reports into variant viewer
migbro/VariantViewer