akshayparopkari / kadambari

A collection of scripts.

Welcome to the kadambari!

Current collection include the following -

Python scripts

• 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   (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

R scripts

• LDA.R
• PCA.R
• upsetR_venn_alternative_example.R

Bash scripts

• concat_R1_R2_files.sh
• get_R1_R2_md5.sh
• integrated_assignment_rnaseq.sh (from CSHL course)
• runpy.sh

kadambari's Issues

Moving frequently used Python scripts to PhyloToAST repo

Context

These Python scripts are used mostly for aiding in downstream analysis and could prove beneficial to PhyloToAST users.

List of scripts to move:

• filter_biom.py
• network_plot_python.py
• network_plots_gephi.py