mjtiv
Bioinformatician Molecular Biologist: PhD in Biochemistry and Molecular Genetics from UVA Masters in Bioinformatics from UD
Paoli, PA
Pinned Repositories
Adjust_Pvalues_Multidimen_Data
Adjusting Pvalues for Multidimensional Data
Annotating_MultiDim_No_Stats_Test
Annotating Multi-Dimensional Results with VEP Results and Corresponding Meta Data
ARB
Compare_VCF_Files
Compares Two VCF Files (Genotype File vs RNA-Seq)
FastqBLAST
Trim and BLAST a random sample of sequences from a FASTQ file
FDR_Corrected_P-value
Code to Run FDR correction of P-values
Job_Arrays_Unix
Example Job Array Code (Torque) With Automatic Loading of Files
ML_MSI_vs_MSS
Machine Learning Using Random Forest to Identify Top Genes for MSI vs MSS Status
VADT
VADT_3.0.0 New and Improved
VCF_Sample_Extractor
Extracts specific samples from a VCF file, creating a new filtered VCF file
mjtiv's Repositories
mjtiv/VADT
VADT_3.0.0 New and Improved
mjtiv/VCF_Sample_Extractor
Extracts specific samples from a VCF file, creating a new filtered VCF file
mjtiv/Adjust_Pvalues_Multidimen_Data
Adjusting Pvalues for Multidimensional Data
mjtiv/Annotating_MultiDim_No_Stats_Test
Annotating Multi-Dimensional Results with VEP Results and Corresponding Meta Data
mjtiv/ARB
mjtiv/Compare_VCF_Files
Compares Two VCF Files (Genotype File vs RNA-Seq)
mjtiv/Comparing_Genotypes_Simplified_Version
Compares to very simplified genotype files for concordance between samples and SNPs.
mjtiv/FastqBLAST
Trim and BLAST a random sample of sequences from a FASTQ file
mjtiv/FastQC_Parser
Parses base quality scores from fastqc for an overall summary report
mjtiv/FDR_Corrected_P-value
Code to Run FDR correction of P-values
mjtiv/Filtering_a_VCF_By_Chromosome
Code to extract a specific chromosome or chromosomes from a VCF file
mjtiv/HFEvsLFE_FisherExactTest
Analyzing Meta Data (HFEvsLFE) using FisherExactTest
mjtiv/Job_Arrays_Unix
Example Job Array Code (Torque) With Automatic Loading of Files
mjtiv/Matching_Files_Program
Program Compares to two files to see if they are identical line by line
mjtiv/Misc_Code
A mixture of different small programs
mjtiv/multicore_demo_program
Demo of how to make a multicore python program
mjtiv/Normalizing_Counts
Normalizing Counts from VRPM and VEP Outputs from VADT analysis.
mjtiv/Parsing_STAR_Output
Program parses through directories of STAR output data and consolidates data
mjtiv/proportional_hypothesis_test
Calculates the p-value when analyzing two populations for statistical differences
mjtiv/Variant_Calling_Pipeline
Example Variant Calling Pipeline with Genome Masking
mjtiv/VEP_Results_Parser_Merger
Parses VEP output results and merges back with original VCF file
mjtiv/ML_MSI_vs_MSS
Machine Learning Using Random Forest to Identify Top Genes for MSI vs MSS Status
mjtiv/DragDrop_Extract_Lines
Program to Extract a Specified Number of Lines from a Large File
mjtiv/Unzip_GZ_File
Unzip a GZ File