Ecosyste.ms: Issues

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

GitHub / bodkan/admixr issues and pull requests

#90 - Error in F3: Following samples are not present

Issue - State: closed - Opened by ans6160 over 1 year ago - 2 comments

#89 - admixr does not find qpDstat

Issue - State: closed - Opened by nicolo-tellini over 1 year ago - 3 comments

#88 - "inbreed:NO means base population must have hets!"

Issue - State: closed - Opened by Agenetics about 2 years ago - 8 comments

#87 - Silence new readr warnings/messages

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

#86 - There seems to have a limit for how many combinations of f4 can be computed at once

Issue - State: closed - Opened by dangliu about 3 years ago - 5 comments

#85 - Move from Travis to Github Actions

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

#84 - Error: Not all three ind/snp/geno files present

Issue - State: closed - Opened by kawu001 about 3 years ago - 6 comments

#83 - custom jackknife

Issue - State: closed - Opened by nicolo-tellini about 3 years ago - 4 comments

#82 - pop: has sample size 1 and inbreed set

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

#81 - filter the geno file for transitions

Issue - State: closed - Opened by mariels over 3 years ago - 3 comments

#80 - f4 stats all zero. Rank 0!. Aborting run

Issue - State: closed - Opened by sahwa over 3 years ago - 4 comments

#79 - Check whitespace handling in EIGENSTRAT paths

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

#78 - bad chrom: conting111,The number of genome conting more than 1000?

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

#77 - qpAdm_rotation problem when nsources >= 3

Issue - State: closed - Opened by paikusuma almost 4 years ago - 3 comments

#76 - Outgroup f3

Issue - State: closed - Opened by murielgb almost 4 years ago - 7 comments

#75 - Describe optional parameter specification in more detail

Issue - State: closed - Opened by bodkan about 4 years ago

#74 - AABB/BBAA sites

Issue - State: closed - Opened by qhelleu about 4 years ago - 1 comment

#73 - admixR and non-standard Chromosome names

Issue - State: closed - Opened by Marvin02860 about 4 years ago - 5 comments

#72 - issue with filter_bed: Inconsistent naming convention

Issue - State: closed - Opened by mgb1985 about 4 years ago - 8 comments

#69 - d() crashes with segmentation fault

Issue - State: closed - Opened by th-al about 4 years ago - 2 comments

#68 - Address the "runnable examples" CRAN issue

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

#67 - CRAN re-submission - add examples, handle printing output properly

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

#66 - ROLLOFF

Issue - State: closed - Opened by foala over 4 years ago - 1 comment

#65 - Make ADMIXTOOLS $PATH checking more robust on different platforms

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

#64 - Fix strange error during CRAN submission

Issue - State: closed - Opened by bodkan over 4 years ago - 4 comments

#63 - Add prototype of qpAdm rotation strategy

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

#62 - Note on the pre-screening functionality

Issue - State: closed - Opened by bodkan over 4 years ago

#61 - Check for correct identity of the "data" argument in all wrappers

Issue - State: closed - Opened by bodkan over 4 years ago - 2 comments

#60 - Fix broken handling of single-source qpAdm runs (fixes #51)

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

#59 - Check truncated output

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

#58 - Implementation of examining log output information

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

#57 - Fix a (potential) issue with log paths on Windows?

Issue - State: open - Opened by bodkan over 4 years ago - 13 comments

#56 - "d" or "f4" statistics output always stderr = 1

Issue - State: closed - Opened by DanielRamos12 over 4 years ago - 2 comments

#55 - An error returning empty dataframe

Issue - State: closed - Opened by aromaze85 over 4 years ago - 2 comments

#54 - Add exhaustive exploration of qpAdm models

Issue - State: closed - Opened by bodkan over 4 years ago - 2 comments

#53 - Use a data.table backend?

Issue - State: closed - Opened by bodkan over 4 years ago - 1 comment

#52 - Deal with ADMIXTOOLS crashes properly

Issue - State: closed - Opened by bodkan over 4 years ago - 6 comments

#51 - Problems with only one source in qpAdm

Issue - State: closed - Opened by bodkan over 4 years ago

#50 - Passing Params to PAR File

Issue - State: closed - Opened by testeranon almost 5 years ago - 3 comments

#49 - admixr result

Issue - State: closed - Opened by smallfishcui almost 5 years ago - 3 comments

#48 - Another duplicated populations error

Issue - State: closed - Opened by bodkan almost 5 years ago

#47 - Deal with truncated log files properly

Issue - State: closed - Opened by bodkan almost 5 years ago

#46 - Differentiating between the two admixr packages

Issue - State: closed - Opened by s-usr about 5 years ago - 1 comment

#45 - f3 has no results from my data

Issue - State: closed - Opened by yimingweng over 5 years ago - 1 comment

#44 - Look into the f3 problems when same population is used twice

Issue - State: closed - Opened by bodkan over 5 years ago

#43 - Implement some of the useful "convertf" functionality

Issue - State: closed - Opened by bodkan over 5 years ago

#42 - Convert 9 <-> NA in read_geno/write_geno

Issue - State: closed - Opened by bodkan almost 6 years ago - 1 comment

#41 - Fast printing of EIGENSTRAT objects

Pull Request - State: closed - Opened by bodkan almost 6 years ago - 1 comment

#40 - Fix parsing errors for duplicated populations

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

#39 - Remove C++ dependencies

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

#38 - C++ implementation of VCF -> EIGENSTRAT conversion

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

#37 - Full implementation of qpWave and qpAdm

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

#36 - Change SNP counting, EIGENSTRAT construction and printing

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

#35 - Check log file before parsing in case ADMIXTOOLS crashes

Issue - State: closed - Opened by bodkan almost 6 years ago - 2 comments

#34 - Add a faster VCF --> EIGENSTRAT parser

Issue - State: closed - Opened by bodkan about 6 years ago - 1 comment

#33 - Add description of adding ADMIXTOOLS to $PATH

Issue - State: closed - Opened by bodkan about 6 years ago

#32 - Add possibility to calculate f3 for all combinations

Issue - State: closed - Opened by bodkan about 6 years ago

#31 - Specify new population labels directly, not via list

Pull Request - State: closed - Opened by bodkan about 6 years ago

#30 - Re-write the package to make it more %>% friendly

Pull Request - State: closed - Opened by bodkan about 6 years ago

#29 - Find a way to specify the paths to ADMIXTOOLS binaries

Issue - State: closed - Opened by bodkan about 6 years ago - 1 comment

#27 - Add R wrapper around `mergeit`

Issue - State: closed - Opened by bodkan about 6 years ago - 1 comment

#26 - Organize exported functions in the reference list

Issue - State: closed - Opened by bodkan about 6 years ago

#25 - Make subset_sites function more generic

Issue - State: closed - Opened by bodkan about 6 years ago - 1 comment

#24 - Make sure that temporary files are properly cleaned up

Issue - State: closed - Opened by bodkan about 6 years ago - 1 comment

#23 - Use `use_pipe`?

Issue - State: closed - Opened by bodkan about 6 years ago

#22 - Make function names more readable

Issue - State: closed - Opened by bodkan over 6 years ago

#21 - Implement better file path handling

Issue - State: closed - Opened by bodkan over 6 years ago

#20 - Deal with the "best" entry in a D statistics output

Issue - State: closed - Opened by bodkan over 6 years ago - 1 comment

#19 - Check for ADMIXTOOLS presence

Issue - State: closed - Opened by bodkan over 6 years ago

#18 - Can we use "SSS" and "DIR" options?

Issue - State: closed - Opened by bodkan over 6 years ago

#17 - Install ADMIXTOOLS into a Travis CI environment for future testing

Issue - State: closed - Opened by bodkan over 6 years ago - 1 comment

#16 - Add an option to save ADMIXTOOLS config/par files with sensible names

Issue - State: closed - Opened by bodkan over 6 years ago - 2 comments

#15 - Let qpDstat calculate the standard errors

Issue - State: closed - Opened by bodkan over 6 years ago - 1 comment

#14 - Use data.table instead of dplyr

Issue - State: closed - Opened by bodkan almost 7 years ago - 1 comment

#13 - Prevent unnecessary warning/message info in read_geno/read_ind/read_snp

Issue - State: closed - Opened by bodkan almost 7 years ago - 1 comment

#11 - Add a tiny utility function for loading and writing EIGENSTRAT data in data.frames

Issue - State: closed - Opened by bodkan almost 7 years ago - 1 comment

#10 - Export VCF from EIGENSTRAT

Issue - State: closed - Opened by bodkan about 7 years ago - 1 comment

#9 - Fix issues with functions from external libraries not being available

Issue - State: closed - Opened by bodkan about 7 years ago - 1 comment

#8 - Add support for the "poplistname" option in qpDstat

Issue - State: closed - Opened by bodkan about 7 years ago - 1 comment

#7 - Check for a presence of individuals in an "ind" file

Issue - State: closed - Opened by bodkan about 7 years ago

#6 - Import from VCF into EIGENSTRAT

Issue - State: closed - Opened by bodkan about 7 years ago - 3 comments

#5 - Convert ADMIXTOOLS warnings to R warnings

Issue - State: closed - Opened by bodkan about 7 years ago - 2 comments

#4 - Convenient function for generating badsnp_file

Issue - State: closed - Opened by bodkan about 7 years ago - 1 comment

#3 - A single function to read all output

Issue - State: closed - Opened by bodkan about 7 years ago

#2 - Add a proper README

Issue - State: closed - Opened by bodkan about 7 years ago

#1 - Add tests for the wrapper functionality

Issue - State: closed - Opened by bodkan about 7 years ago