Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / snitkin-lab-umich/regentrans issues and pull requests

#60 - Question about Estimating Pairwise SNV Threshold Using Mutation Rate

Issue - State: open - Opened by Tonny-zhou over 1 year ago - 1 comment

#60 - Question about Estimating Pairwise SNV Threshold Using Mutation Rate

Issue - State: open - Opened by Tonny-zhou over 1 year ago - 1 comment

#59 - Incorporate Rcpp get_genetic_flow() functions

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

#59 - Incorporate Rcpp get_genetic_flow() functions

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

#58 - Add code to get pairwise day differences between isolates

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment

#58 - Add code to get pairwise day differences between isolates

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment

#57 - Provide example in vignette of intra versus inter patient SNV distance plots

Issue - State: open - Opened by zenalapp about 3 years ago
Labels: documentation, enhancement

#57 - Provide example in vignette of intra versus inter patient SNV distance plots

Issue - State: open - Opened by zenalapp about 3 years ago
Labels: documentation, enhancement

#56 - Add functionality to include multiple patient isolates to calculate Fsp

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: enhancement

#56 - Add functionality to include multiple patient isolates to calculate Fsp

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: enhancement

#55 - Include functionality or example of including multiple patient samples for SNV distance analysis

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: enhancement

#55 - Include functionality or example of including multiple patient samples for SNV distance analysis

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: enhancement

#54 - Fix `check_locs()`

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: bug

#54 - Fix `check_locs()`

Issue - State: closed - Opened by zenalapp about 3 years ago - 1 comment
Labels: bug

#53 - Update website to include link to preprint

Issue - State: closed - Opened by zenalapp over 3 years ago - 1 comment
Labels: documentation, enhancement

#53 - Update website to include link to preprint

Issue - State: closed - Opened by zenalapp over 3 years ago - 1 comment
Labels: documentation, enhancement

#52 - Create preprocessing vignette

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: documentation, enhancement

#52 - Create preprocessing vignette

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: documentation, enhancement

#51 - Make `get_patient_flow()` faster

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#51 - Make `get_patient_flow()` faster

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#50 - Create first release of regentrans

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

#50 - Create first release of regentrans

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

#49 - Make SNV threshold <= instead of <

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

#49 - Make SNV threshold <= instead of <

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

#48 - Update README

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

#48 - Update README

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

#46 - More flexible input for `get_patient_flow()`

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#46 - More flexible input for `get_patient_flow()`

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#45 - Change some variable names

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

#45 - Change some variable names

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

#44 - Rename `get_snv_dists`

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

#44 - Rename `get_snv_dists`

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

#43 - Update vignette

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#43 - Update vignette

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#42 - Fix environmental sample example in vignette

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#42 - Fix environmental sample example in vignette

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#41 - Decrease runtime of `get_facility_fsp` function & tests

Issue - State: closed - Opened by zenalapp over 3 years ago - 1 comment
Labels: enhancement

#41 - Decrease runtime of `get_facility_fsp` function & tests

Issue - State: closed - Opened by zenalapp over 3 years ago - 1 comment
Labels: enhancement

#39 - Have the user remove duplicate patients etc. beforehand

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

#39 - Have the user remove duplicate patients etc. beforehand

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

#38 - Rename output columns for some functions

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

#38 - Rename output columns for some functions

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

#37 - Save data using `usethis::use_data`

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

#37 - Save data using `usethis::use_data`

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

#36 - Update DESCRIPTION

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#36 - Update DESCRIPTION

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#35 - Clean up extras directory

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

#35 - Clean up extras directory

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

#34 - Beef up function documentation

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#33 - Allow more flexibility when `get_pair_types()` used as input

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#33 - Allow more flexibility when `get_pair_types()` used as input

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#32 - Export only user-facing functions

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

#32 - Export only user-facing functions

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

#30 - Set up automatic package check & code reformatting on GitHub

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#30 - Set up automatic package check & code reformatting on GitHub

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#29 - Add code coverage and other stats/info to GitHub page

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#29 - Add code coverage and other stats/info to GitHub page

Issue - State: open - Opened by zenalapp over 3 years ago
Labels: enhancement

#28 - Fix errors, warnings, and notes from `devtools::check()`

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

#28 - Fix errors, warnings, and notes from `devtools::check()`

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

#27 - Update vignette to show manuscript figures

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#27 - Update vignette to show manuscript figures

Issue - State: closed - Opened by zenalapp over 3 years ago
Labels: documentation

#25 - Add unit tests for checks

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

#25 - Add unit tests for checks

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

#24 - Remove duplicate pairs before returning get_snv_dists

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

#24 - Remove duplicate pairs before returning get_snv_dists

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

#23 - Fix get_frac_intra

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

#23 - Fix get_frac_intra

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

#22 - Change first word of all functions to verbs

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

#22 - Change first word of all functions to verbs

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

#19 - [Add to vignette] Code to assign each isolate to a cluster based on the get_clusters output

Issue - State: closed - Opened by kylegontjes over 3 years ago
Labels: documentation, enhancement

#19 - [Add to vignette] Code to assign each isolate to a cluster based on the get_clusters output

Issue - State: closed - Opened by kylegontjes over 3 years ago
Labels: documentation, enhancement

#18 - Add code to plot SNVs vs. time between samples to vignette

Issue - State: closed - Opened by sthiede over 3 years ago - 4 comments
Labels: documentation, enhancement

#18 - Add code to plot SNVs vs. time between samples to vignette

Issue - State: closed - Opened by sthiede over 3 years ago - 4 comments
Labels: documentation, enhancement

#17 - design vignette

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

#17 - design vignette

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

#16 - Return subtrees for get_clusters

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

#16 - Return subtrees for get_clusters

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

#15 - Write tests for outputs

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

#14 - Write tests for checks

Issue - State: closed - Opened by shoffm over 3 years ago
Labels: enhancement

#13 - function to subset to one of each pair from get_snv_dists results

Issue - State: closed - Opened by shoffm over 3 years ago
Labels: enhancement

#12 - Profile get_facility_fsp

Issue - State: closed - Opened by shoffm over 3 years ago
Labels: enhancement

#11 - Create R package

Issue - State: closed - Opened by shoffm almost 4 years ago

#10 - Function to find shared variants between isolates within and between facilities

Issue - State: closed - Opened by shoffm almost 4 years ago
Labels: enhancement

#9 - Function to make count maps

Issue - State: closed - Opened by shoffm almost 4 years ago - 3 comments
Labels: enhancement

#8 - Function to identify pure facility clusters

Issue - State: closed - Opened by shoffm almost 4 years ago
Labels: enhancement

#7 - Function to make summary plots of the data

Issue - State: closed - Opened by shoffm almost 4 years ago
Labels: enhancement

#6 - Function to compare paths of maximum patient flow to pairwise SNV distances

Issue - State: closed - Opened by shoffm almost 4 years ago
Labels: enhancement

#5 - Function to find paths of maximum patient flow

Issue - State: closed - Opened by shoffm almost 4 years ago - 1 comment
Labels: enhancement

#4 - Function to find fraction of intra-facility pairs for different SNV thresholds

Issue - State: closed - Opened by shoffm almost 4 years ago
Labels: enhancement