Pinned Repositories
2022-Rich-RIPseq
AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
ATAC_processing_pipeline
Script set for processing raw ATAC-seq reads into peak calls on Broad Institute
BioinfoFinalProject
Final project for Biol173
dissertation
duit
Course project for CS135 Distributed Software Architecture. Productivity app organizes calendar events as well as deadlines and tasks.
medullo-ecdna
Code accompanying Chapman et al 2021, "The landscape of extrachromosomal circular DNA in medulloblastoma"
oscutils
pedpancan_ecdna
auberginekenobi's Repositories
auberginekenobi/medullo-ecdna
Code accompanying Chapman et al 2021, "The landscape of extrachromosomal circular DNA in medulloblastoma"
auberginekenobi/dissertation
auberginekenobi/oscutils
auberginekenobi/pedpancan_ecdna
auberginekenobi/2022-Rich-RIPseq
auberginekenobi/AmpliconArchitect
Identify one or more connected, focally amplified genomic regions to elucidate the architecture of focal amplifications such as ecDNA.
auberginekenobi/AmpliconSuiteAggregator
Aggregates the results from AmpliconSuite for upload to AmpliconRepository.org
auberginekenobi/ATAC_processing_pipeline
Script set for processing raw ATAC-seq reads into peak calls on Broad Institute
auberginekenobi/BioinfoFinalProject
Final project for Biol173
auberginekenobi/bisb-bootcamp-2020-module08
auberginekenobi/conumee
Enhanced copy-number variation analysis using Illumina DNA methylation arrays -
auberginekenobi/CSE180_Discussion
# Computing readcounts from ENCODE .bam files
auberginekenobi/CycleViz
Visualize outputs of AmpliconArchitect and AmpliconReconstructor in Circos-style images.
auberginekenobi/rcmb56-single-cell
auberginekenobi/DD-Rich-metabolites
auberginekenobi/ecdna-quant
Quantify ecDNA in 10X single-cell ATAC (scATAC-seq) sequencing.
auberginekenobi/fgsea
Fast Gene Set Enrichment Analysis
auberginekenobi/Hospital_handover_annotation
auberginekenobi/InTAD
Correlation of epigenetic signals and genes in TADs
auberginekenobi/lr2rmats
Long read to rMATS
auberginekenobi/mbshh-chd7-kmt2e
auberginekenobi/mbshh-fosl2
auberginekenobi/medulloblastoma-nfi
auberginekenobi/minimalist_bioinformatic_poetry
minimalist bioinformatic poetry. pull requests accepted.
auberginekenobi/PrepareAA
A quickstart tool for AmpliconArchitect. Performs all preliminary steps (alignment, CNV calling, seed interval detection) required prior to running AmpliconArchitect.
auberginekenobi/protocols
auberginekenobi/qsea
QSEA bioconductor package
auberginekenobi/sc-ependymoma
auberginekenobi/ucsd-bisb-unofficial
Unofficial website for UCSD BISB graduate students
auberginekenobi/ucsd-thesis