Nicholas Socci's repositories
BIC-variants_pipeline
BIC@MSKCC Variants Pipeline
Variant-PostProcess
Postprocessing scripts for CBE Variant Pipeline
adagio
Wrapper/accessory scripts for CMO-Tempo
AFICreator
Script to create HALO AFI Files
ChIP-seq
ChIP-seq pipeline
FacetsCNV
2023 version of facets workflow
Goliath
Report01
Halo-Lung
Lung specific project files for Halo study
halo_analysis
Halo project B-101-533
HaloXi
Halo Xi - Lightweight module to process Halo data
integrate
Wrapper code for INTEGRATE application: RNA+DNA SV/Fusion calling
Loki
Workflow for handling CNV events
LPSProgression
Code for Sarcoma Progression Manuscript
MultiCall
Aggregate mutation calls from multiple callers
MusVar
Mouse variant pipeline based on nf-core/sarek
piano
Scripts for running and post-processing forte
Postprocess-Mouse
Mouse Postprocess Version 6 (2021)
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
SMap
S(arek) Map: Scripts to use sarek for mapping WGS samples
ssGSEAAnalysis
ss-gsea analysis from http://dx.doi.org/10.1016/j.ccell.2017.06.003
tempo
CCS research pipeline to process WES and WGS TN pairs
tools-gatk
Wrapper scripts to run GATK
vcf2MafApp
Scripts and info on installing/running VCF2MAF
WGS-workflow
Basic scripts for doing WGS projects