Current collection include the following -
- 1000gpca.py (1000 Genomes Project)
- TSNE.py
- categorized_gramox.py
- combine_data.py
- common_seqs_count.py
- correlation.py
- count_ChrX_variants.py (1000 Genomes Project)
- count_singletons.py (1000 Genomes Project)
- count_variants.py (1000 Genomes Project)
- count_variant_sites.py ย (1000 Genomes Project)
- craigslist_search.py
- dissimilarity_overlap_curve.py
- fill_empty_gramox_data.py
- get_core_ids.py
- get_fastq_quality_stats.py
- gramox_calc.py
- gramox_to_itol_color.py
- grep_count_seqs.py
- haploid_local_ancestry_inference.py (1000 Genomes Project)
- merge_hap_htz_counts.py (1000 Genomes Project)
- merge_with_pear.py
- otu_metadata_db.py
- overlap_comparisons.py
- pct_abd_gramox.py
- In process of moving to PhyloToAST repo.
- plot_MA.py
- plot_ancestry.py
- plot_autosomal_heterozygosity.py (1000 Genomes Project)
- plot_heterozygosity.py (1000 Genomes Project)
- remove_duplicate_genes.py
- run_merge_cmd.py
- run_qual_filter_cmd.py
- trim_five_prime_end_adapters.py
- trim_three_prime_end_adapters.py
- LDA.R
- PCA.R
- upsetR_venn_alternative_example.R
- concat_R1_R2_files.sh
- get_R1_R2_md5.sh
- integrated_assignment_rnaseq.sh (from CSHL course)
- runpy.sh