SchriderLab/Timesweeper

Issues

• timesweeper train : KeyError: 'experiment name'

  #74 opened a year ago by kiwoong-nam
  0

• SHIC features for s regression task

  #70 opened 2 years ago by Lswhiteh
  0

• Add FET module and test

  #65 opened 2 years ago by Lswhiteh
  0

• Module for producing bedfile of allele frequency increase across vcf for IGV/UCSC tracks

  #66 opened 2 years ago by Lswhiteh
  0

• Regression task for s

  #61 opened 2 years ago by Lswhiteh
  0

• Fix up years/gens handling for everything

  #62 opened 2 years ago by Lswhiteh
  0

• Give example ways to generate samp sizes and times with bash

  #58 opened 2 years ago by Lswhiteh
  0

• Add alternative time-series classifiers

  #60 opened 2 years ago by Lswhiteh
  0

• Option to add in BED file of regions to avoid

  #50 opened 2 years ago by Lswhiteh
  0

• Make simulate_stdpopsim more flexible

  #56 opened 2 years ago by Lswhiteh
  0

• RTD Documentation

  #48 opened 2 years ago by Lswhiteh
  0

• Make downstream processes able to deal with only hard/soft instead of all 3 classes

  #53 opened 3 years ago by Lswhiteh
  1

• Separate network for regression tasks

  #69 opened 3 years ago by Lswhiteh
  0

• Log sim params to csv

  #52 opened 3 years ago by Lswhiteh
  0

• Fix Plotting

  #54 opened 3 years ago by Lswhiteh
  0

• Add defaults to arg help messages

  #55 opened 3 years ago by Lswhiteh
  0

• Randomly select allele in cases where allele fixes before sampling

  #63 opened 3 years ago by Lswhiteh
  0

• Flexible k-mer sizes as arg

  #64 opened 3 years ago by Lswhiteh
  0

• Add FET to utility modules

  #59 opened 3 years ago by Lswhiteh
  0

• Monday test

  #57 opened 3 years ago by Lswhiteh
  1

• Refactor so that AFS/HFS is renamed AFT/HFT

  #44 opened 3 years ago by Lswhiteh
  0

• Simplify workflow to be less user calls

  #49 opened 3 years ago by Lswhiteh
  1

• Add in plotting utility module for plotting specific regions

  #51 opened 3 years ago by Lswhiteh
  1

• Artificial missingness

  #45 opened 3 years ago by Lswhiteh
  1

• Setuptools

  #47 opened 3 years ago by Lswhiteh
  1

• Utility script for matching bedtools intersect results back up with raw results

  #46 opened 3 years ago by Lswhiteh
  0

• Alternative solution for HFS data prep to handle two pop sampling

  #24 opened 3 years ago by Lswhiteh
  0

• Streamline sim -> Analysis workflow, including sampling parameterization

  #36 opened 3 years ago by Lswhiteh
  0

• Convert simulation steps into Snakemake Rule

  #26 opened 3 years ago by Lswhiteh
  1

• Merge YAML configs so as to only need one per workflow

  #42 opened 3 years ago by Lswhiteh
  0

• Conf matrices just for central windows and m2 muts

  #35 opened 3 years ago by Lswhiteh
  1

• HDF5 Implementation for condensing data collection and results

  #41 opened 3 years ago by Lswhiteh
  1

• Blocked memory implementation?

  #43 opened 3 years ago by Lswhiteh
  1

• Argparsing and cleanup for FIT

  #30 opened 3 years ago by Lswhiteh
  1

• Make script/file generation more lightweight

  #40 opened 3 years ago by Lswhiteh
  0

• Clean up how we launch sims and process sims

  #32 opened 3 years ago by Lswhiteh
  1

• Organize the tool vs experiments better

  #31 opened 3 years ago by Lswhiteh
  1

• Docstrings for all current scripts

  #33 opened 3 years ago by Lswhiteh
  1

• Clean up old sections of code that are unused with vcf approach

  #34 opened 3 years ago by Lswhiteh
  0

• Rewrite network training to allow for vcf input

  #37 opened 3 years ago by Lswhiteh
  1

• Add option to save center snps to file during vcf preprocessing

  #39 opened 3 years ago by Lswhiteh
  1

• Merge summarize_fit and plot_fit

  #29 opened 3 years ago by Lswhiteh
  0

• Move everything to seaborn

  #38 opened 3 years ago by Lswhiteh
  0

• Do we need to adjust max_snps in haplotype creation?

  #20 opened 3 years ago by Lswhiteh
  1

• Max timepoints arg needs to either be clarified or dynamically set based on the number of gens

  #23 opened 3 years ago by Lswhiteh
  1

• Unify HFS creation across sims and empirical datasets

  #28 opened 3 years ago by Lswhiteh
  1

• Unify HFS creation across sims and empirical datasets

  #27 opened 4 years ago by Lswhiteh
  0

• Force consistent sizing during HFS post-processing

  #25 opened 4 years ago by Lswhiteh
  1

• Huge memory usage from multiprocessing

  #22 opened 4 years ago by Lswhiteh
  1

• Deal with edge cases where haplotype-ms results in inconsistent haplotype lengths

  #21 opened 4 years ago by Lswhiteh
  2