Ecosyste.ms: Issues

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

GitHub / snystrom/memes issues and pull requests

#120 - motif GO

Issue - State: closed - Opened by sugiYag 3 months ago - 1 comment

#119 - rna option not recognised for runStreme

Issue - State: closed - Opened by CharlotteAnne 7 months ago - 2 comments

#118 - Some details about AME tool in MEME Suite

Issue - State: closed - Opened by DengEr-1993 8 months ago - 1 comment

#117 - Maxmium input for RunMeme()?

Issue - State: open - Opened by LuBeifang 9 months ago - 6 comments

#115 - add more examples in runMeme doc

Pull Request - State: open - Opened by seb-mueller 12 months ago

#114 - runmeme breaks when providing control

Issue - State: open - Opened by seb-mueller 12 months ago - 4 comments

#113 - Parse genomic coord behavior changed in 5.5.4

Issue - State: open - Opened by snystrom about 1 year ago

#112 - glam2 for variable length motif discovery

Issue - State: open - Opened by seb-mueller about 1 year ago - 5 comments

#111 - TomTom error with HOCOMOCOv11 mouse database

Issue - State: open - Opened by j-andrews7 about 1 year ago - 3 comments

#110 - Memes download/path issue

Issue - State: closed - Opened by riley-leonard about 1 year ago - 1 comment

#109 - xstreme api

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

#108 - .html was not found.

Issue - State: open - Opened by eladzis over 1 year ago - 16 comments

#107 - issues with streme and tomtom under WSL2/Rstudio server

Issue - State: open - Opened by RaphMet over 1 year ago - 4 comments
Labels: documentation

#106 - Using memes with WSL

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

#105 - path problems

Issue - State: open - Opened by theokirkland almost 2 years ago - 5 comments

#104 - Motif names do not always match motif object name in `runStreme` output

Issue - State: closed - Opened by mniederhuber almost 2 years ago - 18 comments

#103 - Small typo in error message

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

#102 - runStreme() does not return evalue

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

#101 - AME failed with input universalmotif list

Issue - State: closed - Opened by augenbonbon over 2 years ago - 10 comments

#100 - Error in dplyr::mutate() after runMeme

Issue - State: closed - Opened by mwittep over 2 years ago - 3 comments

#99 - error runinng runTomTom

Issue - State: closed - Opened by whywhowhat over 2 years ago - 5 comments

#98 - Failed to open HTML template file

Issue - State: closed - Opened by sshen82 over 2 years ago - 5 comments

#97 - Make informative error message when `parse_genomic_coord` fails

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

#96 - AME output change in v5.4.0

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

#94 - Sequence sort for plot_sequence_heatmap

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

#93 - data viz to quickly check sequence length distribution

Issue - State: open - Opened by snystrom almost 3 years ago
Labels: enhancement

#91 - Write unit tests for new vs old importStremeXML behavior

Issue - State: open - Opened by snystrom almost 3 years ago - 1 comment

#90 - runStreme() error

Issue - State: closed - Opened by ivangalvan almost 3 years ago - 17 comments

#89 - Error: Column `rc` doesn't exist.

Issue - State: closed - Opened by ghost over 3 years ago - 5 comments

#88 - Error in to_df(.) : could not find function "to_df"

Issue - State: closed - Opened by mdozmorov over 3 years ago - 6 comments

#87 - Fix runFimo to work with `readr` update.

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

#86 - runfimo() throws an error when there are no results found and an outdir provided

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

#85 - importStreme assigns weird names to motifs >9

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

#84 - runStreme fails on BStringList

Issue - State: closed - Opened by snystrom over 3 years ago
Labels: bug

#83 - markdown typo

Pull Request - State: closed - Opened by mniederhuber over 3 years ago - 1 comment

#82 - R version requirement

Issue - State: closed - Opened by ywang1993 over 3 years ago - 1 comment

#81 - "~" doesn't expand when passed as database argument

Issue - State: closed - Opened by snystrom over 3 years ago
Labels: bug

#79 - use new universalmotif_df format

Issue - State: closed - Opened by snystrom over 3 years ago - 2 comments

#78 - flyFactorSurvey_cleaned.meme throws duplicated ID warnings in runTomTom

Issue - State: closed - Opened by snystrom over 3 years ago - 3 comments
Labels: bug

#77 - Compatible R version

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

#76 - reenable pkgdown

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

#75 - reenable testthat

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

#74 - reenable covr

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

#73 - fix system.file issue during R CMD Check examples

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

#72 - OS Check to run* functions

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

#71 - Installation issues

Issue - State: closed - Opened by sa95078 about 4 years ago - 1 comment

#70 - is having an "outdir" argument unsafe?

Issue - State: open - Opened by snystrom about 4 years ago

#69 - change README example

Issue - State: open - Opened by snystrom about 4 years ago

#68 - Add support for STREME

Issue - State: open - Opened by snystrom about 4 years ago

#67 - Add support for ENR

Issue - State: open - Opened by snystrom about 4 years ago
Labels: enhancement

#66 - Add motif list column to AME output

Issue - State: open - Opened by snystrom about 4 years ago
Labels: enhancement

#65 - meme_is_installed() fails if directory doesn't exist

Issue - State: closed - Opened by snystrom about 4 years ago - 1 comment
Labels: bug

#64 - check that sequence_input has names if a biostrings object

Issue - State: open - Opened by snystrom about 4 years ago

#63 - change runTomTom method default to Euclidean Distance

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

#62 - re-depend on cmdfun::cmd_list_keep/drop_named

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

#61 - AME plot heatmap sometimes doesn't rank correctly

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

#59 - Export view_motifs method for data.frame

Issue - State: open - Opened by snystrom about 4 years ago

#58 - prune biocViews entry

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

#57 - Find TODO sections & fix if needed

Issue - State: open - Opened by snystrom about 4 years ago

#55 - Unit Test Overhaul

Issue - State: open - Opened by snystrom about 4 years ago
Labels: enhancement

#54 - data viz

Issue - State: open - Opened by snystrom about 4 years ago - 1 comment

#52 - runFimo issues

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

#51 - Changes for cmdfun calls

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

#50 - Improve MEME Suite install process

Issue - State: open - Opened by snystrom over 4 years ago
Labels: enhancement

#49 - Add session_info at the end of vignettes

Issue - State: closed - Opened by snystrom over 4 years ago
Labels: enhancement

#48 - Rename package from {dremeR} to {memes}

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

#47 - test tomtom database with no altname

Issue - State: open - Opened by snystrom over 4 years ago - 2 comments
Labels: enhancement

#46 - add runMeme input test to runTomTom unit tests

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

#45 - use importTomTomXML backend for both import & internal parsing

Issue - State: closed - Opened by snystrom over 4 years ago - 1 comment
Labels: enhancement

#44 - TomTom / Ame / FIMO runs indefinitely if `meme_db` is empty string

Issue - State: closed - Opened by snystrom over 4 years ago - 1 comment
Labels: bug

#43 - Clean up unit tests

Issue - State: open - Opened by snystrom over 4 years ago

#42 - import MEME needs rework

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

#40 - Update runFimo to unlist list input.

Issue - State: open - Opened by snystrom over 4 years ago
Labels: enhancement

#39 - importAME needs a way to guess 'method'

Issue - State: open - Opened by snystrom over 4 years ago
Labels: enhancement

#38 - runTomTom `motif` list column doesn't have names

Issue - State: open - Opened by snystrom over 4 years ago
Labels: bug

#37 - tomtom fails without altid

Issue - State: closed - Opened by snystrom over 4 years ago - 1 comment
Labels: bug

#36 - Release 1.1

Issue - State: open - Opened by snystrom over 4 years ago - 1 comment

#35 - Add `as_universalmotif` method

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

#34 - ame heatmap internal group comparison

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

#33 - helper to convert ame sequences to GRanges

Issue - State: open - Opened by snystrom over 4 years ago
Labels: enhancement

#31 - Experimental: mutate_motifs / update_motifs

Issue - State: closed - Opened by snystrom over 4 years ago - 3 comments
Labels: experimental / feedback needed

#25 - Tomtom output needs revision

Issue - State: closed - Opened by snystrom over 4 years ago - 2 comments
Labels: bug, enhancement

#24 - Vignette: large jobs on cluster w/ rslurm or futures?

Issue - State: closed - Opened by snystrom over 4 years ago
Labels: documentation

#23 - Release 1.0

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

#18 - tomtom warnings & tests

Issue - State: open - Opened by snystrom over 4 years ago
Labels: enhancement

#16 - Vignette: Discover similar motifs, combine, plot pearson cor, search genome w/ FIMO

Issue - State: closed - Opened by snystrom over 4 years ago
Labels: documentation

#15 - Vignette idea: Motif DB query & use as input to runAme/runFimo, etc.

Issue - State: closed - Opened by snystrom over 4 years ago
Labels: documentation

#12 - Mask sequences?

Issue - State: closed - Opened by snystrom over 4 years ago
Labels: wontfix

#9 - Consider Containerizing meme versions

Issue - State: closed - Opened by snystrom almost 5 years ago - 2 comments
Labels: enhancement

#8 - Overhaul summary plot functions.

Issue - State: closed - Opened by snystrom about 5 years ago