SchriderLab/Timesweeper issues and pull requests

#74 - timesweeper train : KeyError: 'experiment name'

Issue - State: open - Opened by kiwoong-nam 11 months ago

#73 - [version] Update version bump.

Pull Request - State: closed - Opened by Lswhiteh almost 2 years ago

#72 - [feat] Big refactor to scenario handling.

Pull Request - State: closed - Opened by Lswhiteh almost 2 years ago

#71 - Lotsa updates

Pull Request - State: closed - Opened by Lswhiteh almost 2 years ago

#70 - SHIC features for s regression task

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: experiment

#69 - Separate network for regression tasks

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature

#68 - Added additional fisher's exact test functionality and cnn hyperparameter tuning code

Pull Request - State: closed - Opened by EliXie212 over 2 years ago - 1 comment

#67 - Major update: Flexible configs and selection coefficients

Pull Request - State: closed - Opened by Lswhiteh over 2 years ago

#66 - Module for producing bedfile of allele frequency increase across vcf for IGV/UCSC tracks

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature, high priority

#65 - Add FET module and test

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature

#64 - Flexible k-mer sizes as arg

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature

#63 - Randomly select allele in cases where allele fixes before sampling

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: bug

#62 - Fix up years/gens handling for everything

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: bug

#61 - Regression task for s

Issue - State: closed - Opened by Lswhiteh over 2 years ago

#60 - Add alternative time-series classifiers

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature

#59 - Add FET to utility modules

Issue - State: closed - Opened by Lswhiteh over 2 years ago
Labels: feature

#58 - Give example ways to generate samp sizes and times with bash

Issue - State: closed - Opened by Lswhiteh almost 3 years ago
Labels: docs

#57 - Monday test

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment
Labels: question

#56 - Make simulate_stdpopsim more flexible

Issue - State: closed - Opened by Lswhiteh almost 3 years ago
Labels: bug

#55 - Add defaults to arg help messages

Issue - State: closed - Opened by Lswhiteh almost 3 years ago
Labels: bug

#54 - Fix Plotting

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

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

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#52 - Log sim params to csv

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

#51 - Add in plotting utility module for plotting specific regions

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#50 - Option to add in BED file of regions to avoid

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

#49 - Simplify workflow to be less user calls

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#48 - RTD Documentation

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

#47 - Setuptools

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#46 - Utility script for matching bedtools intersect results back up with raw results

Issue - State: open - Opened by Lswhiteh almost 3 years ago

#45 - Artificial missingness

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#44 - Refactor so that AFS/HFS is renamed AFT/HFT

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

#43 - Blocked memory implementation?

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment
Labels: feature, low priority

#42 - Merge YAML configs so as to only need one per workflow

Issue - State: closed - Opened by Lswhiteh almost 3 years ago

#41 - HDF5 Implementation for condensing data collection and results

Issue - State: closed - Opened by Lswhiteh almost 3 years ago - 1 comment

#40 - Make script/file generation more lightweight

Issue - State: closed - Opened by Lswhiteh about 3 years ago

#39 - Add option to save center snps to file during vcf preprocessing

Issue - State: closed - Opened by Lswhiteh about 3 years ago - 1 comment
Labels: feature

#38 - Move everything to seaborn

Issue - State: open - Opened by Lswhiteh about 3 years ago
Labels: feature

#37 - Rewrite network training to allow for vcf input

Issue - State: closed - Opened by Lswhiteh about 3 years ago - 1 comment
Labels: feature

#36 - Streamline sim -> Analysis workflow, including sampling parameterization

Issue - State: closed - Opened by Lswhiteh about 3 years ago

#35 - Conf matrices just for central windows and m2 muts

Issue - State: closed - Opened by Lswhiteh about 3 years ago - 1 comment
Labels: feature

#34 - Clean up old sections of code that are unused with vcf approach

Issue - State: closed - Opened by Lswhiteh about 3 years ago

#33 - Docstrings for all current scripts

Issue - State: closed - Opened by Lswhiteh about 3 years ago - 1 comment
Labels: docs

#32 - Clean up how we launch sims and process sims

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#31 - Organize the tool vs experiments better

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#30 - Argparsing and cleanup for FIT

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#29 - Merge summarize_fit and plot_fit

Issue - State: closed - Opened by Lswhiteh over 3 years ago

#28 - Unify HFS creation across sims and empirical datasets

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: bug, high priority

#27 - Unify HFS creation across sims and empirical datasets

Issue - State: closed - Opened by Lswhiteh over 3 years ago
Labels: bug, high priority

#26 - Convert simulation steps into Snakemake Rule

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: feature, high priority

#25 - Force consistent sizing during HFS post-processing

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#24 - Alternative solution for HFS data prep to handle two pop sampling

Issue - State: closed - Opened by Lswhiteh over 3 years ago
Labels: feature, low priority

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

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: bug, low priority

#22 - Huge memory usage from multiprocessing

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

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

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 2 comments
Labels: bug, question, high priority

#20 - Do we need to adjust max_snps in haplotype creation?

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: question, low priority

#19 - Variable Sample Size for given timepoints

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: feature, high priority

#18 - Example output from each function.

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment
Labels: low priority, docs

#17 - Figure out how this is going to run on clusters/computers of different types.

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 3 comments
Labels: feature, low priority

#16 - Refactor to be Experiment-First program

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#15 - Add option for sampling from last timepoint

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#14 - Update slimfile specification in args

Issue - State: closed - Opened by Lswhiteh over 3 years ago - 1 comment

#13 - Update docs

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: low priority, docs

#12 - Sort haplotype matrix by most common hap at any point, not just the end

Issue - State: closed - Opened by Lswhiteh almost 4 years ago - 1 comment

#11 - Accuracy vs training set size

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: experiment

#10 - Ancestral state rebuilding using phylo approaches before time series inference

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: experiment

#9 - Some model of archaic human pops

Issue - State: closed - Opened by Lswhiteh almost 4 years ago - 2 comments
Labels: experiment

#8 - Paremeter inference

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: experiment

#7 - Add in variable time-sampling intervals

Issue - State: closed - Opened by Lswhiteh almost 4 years ago - 1 comment

#6 - Add in variable window searches for sweep discovery

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: feature, low priority, experiment

#5 - Nextflow pipeline

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: feature

#4 - Refactor preprocessing to be larger job submissions

Issue - State: closed - Opened by Lswhiteh almost 4 years ago
Labels: bug

#3 - Data generator for npz files

Issue - State: closed - Opened by Lswhiteh about 4 years ago - 1 comment
Labels: feature

#2 - Change method of saving haplotype data to be faster

Issue - State: closed - Opened by Lswhiteh about 4 years ago
Labels: bug, feature

#1 - Update networks.py to use haplotype data

Issue - State: closed - Opened by Lswhiteh about 4 years ago - 1 comment
Labels: feature

GitHub / SchriderLab/Timesweeper issues and pull requests