cbg-ethz/pyggdrasil issues and pull requests

#89 - Division by Zero in scphylo ancestor-descendant distance

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🐛 bug, ❗priority: medium, ⏰ time estimate: S

#88 - Revise Visualisation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, action: refactor, ❗priority: high, 🧩 in sprint, ⏰ time estimate: M

#87 - Advanced Metric Calculator Classes

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#86 - Implement Distance Utilities

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#85 - Gordon/implement distance utilities rebase

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#84 - Fixing Tree Move Bugs #2

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: high, ⏰ time estimate: M

#83 - Investigating Bug - Tree breaking apart 2

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🐛 bug, ❗priority: high, 🧩 in sprint

#82 - Implement Distance Utilities

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#81 - Add Snakemake Format Checker

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🕮 action: documentation, 🦾 action: enhancement, ❗priority: low, ⏰ time estimate: S

#80 - Revise MCMC Script 2

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint, ⏰ time estimate: M

#79 - Revise MCMC Script

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment

#78 - Test Tree Generation and Cell Simulation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, ❗priority: high, 🧩 in sprint, ⏰ time estimate: S

#77 - Implement Full Snakemake

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint

#76 - MARK02 - Convergence issues

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🧪 action: experiment

#75 - MARK03 - Better Initialisation Strategies

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🧪 action: experiment

#74 - Implement Distance Utilities

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🦾 action: enhancement

#73 - MARK01: How well does HUNTRESS work?

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🧪 action: experiment

#72 - Revise Visualisation / Add Script

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint

#71 - MCMC Analyser Script

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint

#70 - Revising MCMC run script - switch to snakemake/pedantic config #69

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: low, 🧩 in sprint, ⏰ time estimate: S

#69 - Switch to snakemake config and pedantic models in MCMC run

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: S

#68 - Write Script for Huntress Tree Generation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: M

#67 - Test Tree and Cell Simulation Together

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: ❗priority: high, 🧩 in sprint, ⏰ time estimate: S

#66 - Revise MCMC Script

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🦾 action: enhancement, action: refactor, ❗priority: high, 🧩 in sprint

#65 - Refactor `tree_from_tree_node` to be static of `Tree`

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: action: refactor, ❗priority: low, ⏰ time estimate: S

#64 - Revised version of Cell Simulation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, action: refactor, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: M

#63 - Write Script for Tree Generation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: S

#62 - Refactor generate Trees to use TreeNode format as public API

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, action: refactor, ❗priority: medium, 🧩 in sprint

#61 - Write Script for Tree Generation

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint

#60 - Write Script to make huntress initial tree from cell simulation data

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#59 - Refactor generate Trees to use TreeNode format as public API

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: action: refactor, ❗priority: high, 🧩 in sprint, ⏰ time estimate: S

#58 - Revert Temporary Fixed Version of Pyright and cyvcf2

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: ❗priority: low, ⏰ time estimate: S

#57 - Make PYright version flexible again

Issue - State: closed - Opened by gordonkoehn over 1 year ago

#56 - Rewrite cell_simulation.py to give only one tree

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, action: refactor, ❗priority: medium, 🧩 in sprint

#55 - Creating modular ID classes for (Trees, Cell Simulations, MCMC Run) for file naming

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#54 - Unique, Flexible File naming for Trees, Cell Simulations and MCMC Samples

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#53 - Devise a scalable workflow / structure to analyze and save all

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint

#52 - Tree Generation (Random, Deep, Star)

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint

#51 - Generate Different Tree Types

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, 🧩 in sprint

#50 - Recommended Reading Convergence/Dimensionality Reduction

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🕮 action: documentation, ❗priority: low, ⏰ time estimate: L, 🧪 action: experiment

#49 - Healing the tree of life - fixing _swap_subtrees_move_ for same lineage moves.

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, 🦾 action: enhancement, ❗priority: high

#48 - Investigate Potential Bug in MCMC Tree Moves

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 4 comments
Labels: 🐛 bug, ❗priority: high

#47 - Consider cleaning up `tree_utils`

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: action: refactor, ❗priority: low, ⏰ time estimate: S

#46 - Temporary fix of pyright version - some troubles with iteration of tree objects.

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug

#45 - Temporary fixing of pyright version

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug

#44 - Fix variable confusion `n_trees` / `n_cells` in Snakemake workflow params

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🐛 bug

#43 - Fix `n_trees` / `n_cells` typo in Snakemake workflow params

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug

#42 - Visualisation of MCMC iteration/time series

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 6 comments
Labels: 🦾 action: enhancement, ❗priority: high, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: L

#41 - Ponder about Estimating Probabilities with Missing Data

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago

#40 - Resolve dependency issue

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago - 1 comment

#39 - Investigate dependency issue

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago

#38 - Visualization Groundwork and Tree Comparison

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, help wanted, ❗priority: high, 🧩 in sprint, ⏰ time estimate: M

#37 - Unify conventions of mutation matrices

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🐛 bug, action: refactor, ❗priority: high, 🧩 in sprint

#36 - Consistent naming of FNR and FPR

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🐛 bug, action: refactor

#35 - Consider using hierarchical configurations

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: low

#34 - Ponder about Estimating Probabilities with Missing Data

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 4 comments
Labels: ⏰ time estimate: S

#33 - Proof of Concept of Running Workflow on Euler with SLURM / Mamba

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🧩 in sprint, ⏰ time estimate: M

#32 - 🏃 Sprint 2: First Experiment

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 1 comment
Labels: 🏃sprint plan

#31 - Make sure we follow one convention of mutation matrices

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 4 comments
Labels: 🐛 bug, action: refactor, ❗priority: high, ⏰ time estimate: M

#30 - Consistent naming of FNR and FPR

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 2 comments
Labels: 🐛 bug, action: refactor, ❗priority: high, ⏰ time estimate: S

#29 - Add utilities from scPhylo

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: high, 🧩 in sprint, ⏰ time estimate: M

#28 - Full MCMC simulation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#27 - Tree Visualisation

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 3 comments
Labels: 🦾 action: enhancement

#26 - Explore the MCMC sampler for a bimodal distribution

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: ❗priority: medium

#25 - Explore the MCMC sampler for a bimodal distribution

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 8 comments
Labels: ❗priority: low, 🧩 in sprint, ⏰ time estimate: M, 🧪 action: experiment

#24 - Setting the simulations

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 2 comments
Labels: ❗priority: high, 🧩 in sprint, ⏰ time estimate: L

#23 - Visualisation of time series

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 9 comments
Labels: 🦾 action: enhancement, 🧩 in sprint, ⏰ time estimate: M

#22 - Add a function taking two TreeNodes and returning distance

Issue - State: closed - Opened by pawel-czyz over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: M

#21 - Tree visualisation

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 2 comments
Labels: 🦾 action: enhancement, 🧩 in sprint, ⏰ time estimate: S

#20 - Full MCMC simulation

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 6 comments
Labels: 🦾 action: enhancement, 🧩 in sprint, ⏰ time estimate: L

#19 - Add the log-probability function

Issue - State: closed - Opened by pawel-czyz over 1 year ago - 2 comments
Labels: 🦾 action: enhancement, 🧩 in sprint, ⏰ time estimate: M

#18 - 🏃 Sprint 1: MCMC finding the trees and plotting convergence

Issue - State: closed - Opened by pawel-czyz over 1 year ago
Labels: 🏃sprint plan

#17 - Log Likelihood of a Tree

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#16 - Adding Workflow Management

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🦾 action: enhancement

#15 - Adjust _prune_and_reattach_proposal to use fixed size arrays

Issue - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement, ❗priority: low

#14 - Add Tests for MCMC Tree Moves

Issue - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: low

#13 - Move scripts outside of the package

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago

#12 - MCMC kernel for SCITE inference

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#11 - Cell Simulation Script

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#10 - Add MCMC template for SCITE inference

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#9 - Attach Cells To Tree

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago - 2 comments
Labels: 🦾 action: enhancement

#8 - Add installation instructions

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago
Labels: 🕮 action: documentation

#7 - Add the distance interface

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago - 2 comments
Labels: 🦾 action: enhancement

#6 - Add noise to perfect mutation matrix

Pull Request - State: closed - Opened by gordonkoehn over 1 year ago
Labels: 🦾 action: enhancement

#5 - Generic class for trees

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago - 1 comment
Labels: 🦾 action: enhancement

#4 - Sketch cell sampling from mutation tree

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago

#3 - Add Pyright to CI

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago

#2 - Add HUNTRESS

Issue - State: closed - Opened by pawel-czyz over 1 year ago
Labels: 🦾 action: enhancement, ❗priority: medium, 🧩 in sprint, ⏰ time estimate: L

#1 - Set up CI

Pull Request - State: closed - Opened by pawel-czyz over 1 year ago

GitHub / cbg-ethz/pyggdrasil issues and pull requests