Ecosyste.ms: Issues

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GitHub / wuaipinglab/sitePath issues and pull requests

#30 - How to choose the parameters (e.g Nmin and minSNP)?

Issue - State: open - Opened by virologist about 2 years ago - 4 comments

#29 - Bugfix: invalid parallel mutation at the divergent node of lineages

Pull Request - State: closed - Opened by Takkoona over 3 years ago
Labels: bug

#28 - The site of label is wrong

Issue - State: open - Opened by hyzhou1990 almost 4 years ago

#27 - Apply multiprocess for computational heavy functions

Pull Request - State: closed - Opened by Takkoona almost 4 years ago
Labels: enhancement

#26 - Guess sequence type based on ATCG proportion

Pull Request - State: closed - Opened by Takkoona almost 4 years ago
Labels: enhancement

#25 - The wrong determined fixed sites

Issue - State: open - Opened by hyzhou1990 about 4 years ago
Labels: bug

#24 - Auto determining the sequence type

Issue - State: closed - Opened by hyzhou1990 about 4 years ago
Labels: enhancement

#23 - Change the way of combining fixation mutation from multiple lineages

Pull Request - State: closed - Opened by Takkoona about 4 years ago
Labels: bug

#22 - Duplicated label for the same fixation mutation

Issue - State: closed - Opened by Takkoona about 4 years ago
Labels: bug

#21 - Consistent fixation result among lineages

Pull Request - State: closed - Opened by Takkoona about 4 years ago
Labels: bug, enhancement

#20 - Add a progress bar for computational heavy functions

Issue - State: closed - Opened by hyzhou1990 about 4 years ago - 2 comments
Labels: enhancement, wontfix

#19 - CD-HIT like clustering method on site polymorphism for finer lineage resolving

Pull Request - State: closed - Opened by Takkoona about 4 years ago
Labels: enhancement

#17 - Option for sequence type and excluding gap or ambiguous character

Pull Request - State: closed - Opened by Takkoona over 4 years ago
Labels: enhancement

#16 - Add function to predict sites having mutated on multiple lineage in parallel

Pull Request - State: closed - Opened by Takkoona over 4 years ago
Labels: enhancement

#15 - Rewrite old 'plotSingleSite' functions using ggtree

Pull Request - State: closed - Opened by Takkoona over 4 years ago

#14 - Allow non-bifurcation when merging path and new internal functions

Pull Request - State: closed - Opened by Takkoona over 4 years ago

#13 - The mutation shows up near the root of the tree

Issue - State: closed - Opened by Takkoona over 4 years ago
Labels: bug

#12 - Site numbering can only be applied to some of the type

Issue - State: open - Opened by Takkoona over 4 years ago
Labels: enhancement, good first issue

#11 - The '.mergeClusters' strategy amendment

Pull Request - State: closed - Opened by Takkoona over 4 years ago
Labels: bug

#10 - Tree bifurcation check and new '.mergeClusters' strategy

Pull Request - State: closed - Opened by Takkoona over 4 years ago
Labels: bug

#9 - Error linked to similarity argument in lineagePath function

Issue - State: closed - Opened by hyzhou1990 over 4 years ago
Labels: bug, good first issue

#8 - Minor fixes on paragraphs 64, 75, 87, 99

Pull Request - State: closed - Opened by kant over 4 years ago

#7 - Introduce resampling approach for finding fixation

Pull Request - State: closed - Opened by Takkoona about 5 years ago

#6 - Use minimum entropy for finding both single and multiple fixation

Pull Request - State: closed - Opened by Takkoona over 5 years ago
Labels: enhancement

#5 - Improvement for finding the sites with multiple fixations

Pull Request - State: closed - Opened by Takkoona over 5 years ago
Labels: enhancement

#4 - 'multiFixationSites' function using minimum entropy

Pull Request - State: closed - Opened by Takkoona over 5 years ago
Labels: enhancement

#3 - Add functionality for detecting site with multiple fixation events

Pull Request - State: closed - Opened by Takkoona almost 6 years ago

#2 - Integrate sequence alignment into tree object

Pull Request - State: closed - Opened by Takkoona almost 6 years ago

#1 - Detection of fixation site does not require predicted ancestral sequences

Pull Request - State: closed - Opened by Takkoona over 6 years ago