Alec Steep's repositories
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
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
20191205_pilot-snp-compare_steep
Bird's-eye Genos
20200309_rna-seq_steep
Examination of MoTrPAC RNA-Seq
20220214_vcf-annotation_steep
SNP Alleles in Selective Sweep Regions
Agriplex_Targeted_DNASeq
Validation of nonsynonymous snv and indel calls in Gallus gallus Marek's disease lymphomas
All_we_do_is_win
A simple strategy for winning internal funding at Umich
bermuda_fastq2bam
Preprocessing and mapping whole genome sequencing illumina reads from Bermuda chickens
bermuda_germline_snps_indels
This pipeline aims to call hard-filtered germline snps from Bermuda chickens.
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.
IKZF1_paper_code
Bioinformatic analysis for IKZF1 paper
MDV_US_Strains
Identification of Marek’s disease virus genes associated with virulence of US strains
mutenrich_dev
A Somatic Mutation Enrichment Pipeline
random_forest_indels
Random Forest Model to Predict "Real" Indels
sample_organization
Explanation of tumor sampling, storage, and testing
SRA_Example
An Example Submission to the SRA
Supplementary_information
Supplementary information
umich_salary
Umich Salary Data