Software/Tools
Software/Tools
Embedded Files
Our services provide bioinformatics support that process raw genomic data that contribute to clinical research hospital wide through Mass General Brigham (ie. Partners)
Our services provide bioinformatics support that process raw genomic data that contribute to clinical research hospital wide through Mass General Brigham (ie. Partners)
Pipelines
Pipelines
mRNA-Seq-Taffeta
mRNA-Seq-Taffeta
Bioinformatics can download, align and provide QC for NGS RNASeq Data
Bioinformatics can download, align and provide QC for NGS RNASeq Data
miRNA-Seq BCBIO
miRNA-Seq BCBIO
Bioinformatics can download, align and quantify NGS miRNASeq data using the BCBIO small rnaseq pipeline developed by Lorena Pantano.
Bioinformatics can download, align and quantify NGS miRNASeq data using the BCBIO small rnaseq pipeline developed by Lorena Pantano.
GWAS-eQTL Colocalization
GWAS-eQTL Colocalization
Bioinformatics can run a colocalization analysis of GWAS and eQTL results data.
Bioinformatics can run a colocalization analysis of GWAS and eQTL results data.
RNASeq Quantification - Count QC Ap
RNASeq Quantification - Count QC Ap
Bioinformatics can generate pvalues for differential expression contrasts from aligned BAM files.
Bioinformatics can generate pvalues for differential expression contrasts from aligned BAM files.
Methyl-Seq CpGiant Pipeline
Methyl-Seq CpGiant Pipeline
Bioinformatics can generate a list of called CpG sites from NGS data.
Bioinformatics can generate a list of called CpG sites from NGS data.
ATAC-Seq
ATAC-Seq
Pipeline under development.
Pipeline under development.
Fastq bowtie alignment pipeline
Fastq bowtie alignment pipeline
Fastq files can be aligned with bowtie, and basic QC information can be computed.
Fastq files can be aligned with bowtie, and basic QC information can be computed.
RNASeq - Salmon Count Pipeline
RNASeq - Salmon Count Pipeline
Fastq files can be quantified with salmon to produce count matrices, skipping alignment.
Fastq files can be quantified with salmon to produce count matrices, skipping alignment.
GWAS dn8 pipeline
GWAS dn8 pipeline
Epacts, Metal and Plink GWAS results files can be put in dn8 format.
Epacts, Metal and Plink GWAS results files can be put in dn8 format.
Microbiome - pathseq
Microbiome - pathseq
An abundance table and display app can be created from fastq files.
An abundance table and display app can be created from fastq files.
scRNASeq BCBIO
scRNASeq BCBIO
Single Cell BCBIO Pipeline under development.
Single Cell BCBIO Pipeline under development.
Chipseq - Epigentek
Chipseq - Epigentek
Peak files can be created from fastq files.
Peak files can be created from fastq files.
MPRA Pipeline
MPRA Pipeline
Counts for each 11bp prefix can be generated from fastq data.
Counts for each 11bp prefix can be generated from fastq data.
GoShifter
GoShifter
Bioinformatics can generate pvalues for different SNPs for all types of genomic annotations
Bioinformatics can generate pvalues for different SNPs for all types of genomic annotations
GWAS QC
GWAS QC
Generate QC Reports for GWAS-scale genotype datasets in plink format; transform Illumina full-call reports into plink format
Generate QC Reports for GWAS-scale genotype datasets in plink format; transform Illumina full-call reports into plink format
SHAPEIT/Phase Pipeline
SHAPEIT/Phase Pipeline
Produce Phased Haplotypes from GWAS data; suitable for input to IMPUTE2
Produce Phased Haplotypes from GWAS data; suitable for input to IMPUTE2
In-House Imputation
In-House Imputation
Run a chunked imputation using IMPUTE2 with phased haplotypes and one of several reference haplotype panels
Run a chunked imputation using IMPUTE2 with phased haplotypes and one of several reference haplotype panels
UMich Imputation
UMich Imputation
Generate cleaned VCF-format files suitable for upload and imputation on the UMich Imputation Server; some tools to help with downstream processing and post-imputation QC
Generate cleaned VCF-format files suitable for upload and imputation on the UMich Imputation Server; some tools to help with downstream processing and post-imputation QC
16S Microbiome
16S Microbiome
Produce OTU Abundance tables against GreenGenes from raw fastq data received from PPM
Produce OTU Abundance tables against GreenGenes from raw fastq data received from PPM
WGS/Microbiome
WGS/Microbiome
ALPHA: Run HUMANN2 against WGS Microbiome Data
ALPHA: Run HUMANN2 against WGS Microbiome Data
Liftover
Liftover
Liftover genotype datasets from older to newer genomes
Liftover genotype datasets from older to newer genomes
PCA
PCA
Calculate principal components using several methods: Eigenstrat, TRACE, flashPCA2, flashPCA2 w/ Projection, upload to LASER?
Calculate principal components using several methods: Eigenstrat, TRACE, flashPCA2, flashPCA2 w/ Projection, upload to LASER?
Page updated
Report abuse