Pinned Repositories
DFCI-CCCB-GATK-pipeline
Bash based GATK pipeline to process sequences on the general compute servers
PAINS-train
Machine learning process to identify pan assay interference compounds.
sdRNAPeaksIdentification
Various scripts for handling peak calling of short RNA.
DFCI-CCCB-GATK-Cloud-pipeline
Pipeline for Cloud platfor of DFCI CCCB for GATK based variant calling.
HLA_epitope_prediction_from_WES
HLA epitope prediction from WES.
DFCI-CCCB-TumorNormalPair-WES-pipeline
A pipeline for processing tumor normal WES data with VarScan2.
amplicon_stats
From "cut" DNA, identify specificity of enrichment of "cut" amplicon over background, partuclarly around cut loci.
ChiXCHI
Software for identifying cross-contaminant samples in high throughput sequencing.
CLEAR-CLIP_chimera-masking
Demultiplexing of chimeras from CLEAR-CLIP protocol samples.
DFCI-CCCB-Plexwell-pipeline
Processing and output of plexwell amplicon sequencing.
dkdeconti's Repositories
dkdeconti/PAMP_CpG_calculator
Identifies pathogen-associated molecular patterns specifically by CpG divergence from expected.
dkdeconti/sdRNAPeaksIdentification
Various scripts for handling peak calling of short RNA.
dkdeconti/ChiXCHI
Software for identifying cross-contaminant samples in high throughput sequencing.
dkdeconti/path_profiles
dkdeconti/star-paired-align-and-dge
WDL-based pipeline for analysis of paired-end Illumina data. Uses STAR aligner and performs a basic contrast using DESeq2
dkdeconti/amplicon_stats
From "cut" DNA, identify specificity of enrichment of "cut" amplicon over background, partuclarly around cut loci.
dkdeconti/DFCI-CCCB-GATK-Cloud-pipeline
Pipeline for Cloud platfor of DFCI CCCB for GATK based variant calling.
dkdeconti/DFCI-CCCB-Plexwell-pipeline
Processing and output of plexwell amplicon sequencing.
dkdeconti/HLA_epitope_prediction_from_WES
HLA epitope prediction from WES.
dkdeconti/DFCI-CCCB-TumorNormalPair-WES-pipeline
A pipeline for processing tumor normal WES data with VarScan2.
dkdeconti/General_bioinformatics_tools
General tools for bioinformatics such as creation of heatmaps, VCF parsing, etc.
dkdeconti/DFCI-CCCB-Random_tools
Random assortment of useful scripts
dkdeconti/CLEAR-CLIP_chimera-masking
Demultiplexing of chimeras from CLEAR-CLIP protocol samples.
dkdeconti/project_flow_control
An electron program for handling project control.
dkdeconti/ZipGen
Algorithm(s) for merging two arbitrary proteins to create overlapping genes.
dkdeconti/DFCI-CCCB-GATK-pipeline
Bash based GATK pipeline to process sequences on the general compute servers
dkdeconti/DFCI-CCCB-Queue-for-LSF
A Queue based Qscript for scatter gather of Haplotype Caller and downstream GATK analyses for Partners LSF
dkdeconti/PAINS-train
Machine learning process to identify pan assay interference compounds.