steepale
Working on that quantitative skillset. MoTrPAC (https://motrpac.org/)
University of MichiganAnn Arbor, MI
Pinned Repositories
20190811_fastq2bam_steep
A fastq to bam workflow
20190817_rbaseubuntu_steep
A base R Image on Ubuntu
20190818_music2_steep
A MuSiC2 workflow in CWL and Dockerized images
20190819_roirscript_steep
A quick R script to parse data in GTF format
20190822_bulkrnaseq-example_steep
Example code from bulk RNASeq analysis
20200915_metabolomics-pass1a
PASS1A MoTrPAC Metabolomics
20210826_pass1a-original_steep
Processing of UMich metabolomics PASS1A data prior to drift correction
Docker_MuSiC2
Docker image for MuSiC2
provean
Analysis of validated variants and their predicted effect on gene product (specifically, protein) function
steepale's Repositories
steepale/20200915_metabolomics-pass1a
PASS1A MoTrPAC Metabolomics
steepale/20210826_pass1a-original_steep
Processing of UMich metabolomics PASS1A data prior to drift correction
steepale/Docker_MuSiC2
Docker image for MuSiC2
steepale/provean
Analysis of validated variants and their predicted effect on gene product (specifically, protein) function
steepale/20190811_fastq2bam_steep
A fastq to bam workflow
steepale/20190817_rbaseubuntu_steep
A base R Image on Ubuntu
steepale/20190818_music2_steep
A MuSiC2 workflow in CWL and Dockerized images
steepale/20190819_roirscript_steep
A quick R script to parse data in GTF format
steepale/20190822_bulkrnaseq-example_steep
Example code from bulk RNASeq analysis
steepale/20191205_pilot-snp-compare_steep
Bird's-eye Genos
steepale/20200309_rna-seq_steep
Examination of MoTrPAC RNA-Seq
steepale/20220214_vcf-annotation_steep
SNP Alleles in Selective Sweep Regions
steepale/Agriplex_Targeted_DNASeq
Validation of nonsynonymous snv and indel calls in Gallus gallus Marek's disease lymphomas
steepale/All_we_do_is_win
A simple strategy for winning internal funding at Umich
steepale/bermuda_fastq2bam
Preprocessing and mapping whole genome sequencing illumina reads from Bermuda chickens
steepale/bermuda_germline_snps_indels
This pipeline aims to call hard-filtered germline snps from Bermuda chickens.
steepale/custom_filtering_and_mutated_gene_annotation
Extension of filtering of somatic non-synonymous SNVs and INDELs (custom filtering strategy using samtools mpileup) followed by custom functional annotation of each variant and the gene they are mutated in.
steepale/databases
Documentation for extraction of relevant annotation to MDV project from publicly available databases
steepale/IKZF1_paper_code
Bioinformatic analysis for IKZF1 paper
steepale/MDV_proj
Scripts used in MDV project
steepale/MDV_US_Strains
Identification of Marek’s disease virus genes associated with virulence of US strains
steepale/mutenrich_dev
A Somatic Mutation Enrichment Pipeline
steepale/nf-core-mutenrich
steepale/random_forest_indels
Random Forest Model to Predict "Real" Indels
steepale/rotation
steepale/sample_organization
Explanation of tumor sampling, storage, and testing
steepale/SRA_Example
An Example Submission to the SRA
steepale/Supplementary_information
Supplementary information
steepale/umich_salary
Umich Salary Data
steepale/wgsfastqtobam