Ecosyste.ms: Issues

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GitHub / adamewing/methylartist issues and pull requests

#99 - Problem running run_tests.sh

Issue - State: open - Opened by IanCodes about 2 months ago

#98 - Choose legend position

Issue - State: open - Opened by silvia-s 3 months ago - 2 comments
Labels: enhancement

#97 - Issue with updating to version 1.3.1

Issue - State: open - Opened by ntillquist 3 months ago - 6 comments

#95 - differentiated 5mC and 5hmC, or excluding one of the two

Issue - State: closed - Opened by mvukk 4 months ago - 1 comment

#94 - Methylartist locus hangs while building alignment plot

Issue - State: closed - Opened by aruta321 4 months ago - 2 comments

#93 - Displaying BED Files as Separate Tracks

Issue - State: open - Opened by mllamasl 4 months ago - 3 comments

#92 - Highlight in `locus` with different colors

Issue - State: open - Opened by skranz0 4 months ago - 1 comment

#91 - Highlighting a region breaks the `locus` plot

Issue - State: closed - Opened by skranz0 5 months ago - 3 comments

#90 - What are the pale regions in the smoothed LLR line in `locus`?

Issue - State: closed - Opened by skranz0 5 months ago - 2 comments

#89 - N/A output

Issue - State: open - Opened by vyx-lucy-kaplun 5 months ago - 1 comment

#88 - Dorado .bam files to visualize

Issue - State: open - Opened by ramnageena11 5 months ago - 1 comment

#87 - Add --csi argument to support CSI index

Pull Request - State: closed - Opened by cmdcolin 6 months ago - 3 comments

#86 - Unsupported modifications

Issue - State: open - Opened by Ge0rges 7 months ago

#85 - `locus` cannot find csi-index for gtf, but my file is out off range for tbi

Issue - State: closed - Opened by skranz0 7 months ago - 8 comments

#84 - combine WGBS db file and dorado modbase bam file together

Issue - State: open - Opened by xzhuo 7 months ago
Labels: enhancement

#83 - segplot tsv file error

Issue - State: open - Opened by Manorma1234-tech 7 months ago

#82 - Strand specific plots

Issue - State: open - Opened by dmsoanes 8 months ago

#81 - Failure to run wgmeth

Issue - State: open - Opened by IanCodes 8 months ago - 13 comments

#80 - Is There an Option to Hide or Resize the Legend in methylartist?

Issue - State: closed - Opened by evalopezf 8 months ago - 7 comments

#79 - Saving plots into pdf

Issue - State: closed - Opened by Machadum 9 months ago - 7 comments

#78 - Question about output comprehension

Issue - State: open - Opened by VahidJavaran 9 months ago - 2 comments

#77 - Methylartist noes not recognize cram index

Issue - State: closed - Opened by vyx-lucy-kaplun 9 months ago - 4 comments

#76 - Issue methylartist locus

Issue - State: closed - Opened by OceaneMion 9 months ago - 2 comments

#75 - Question regarding name of chromosome

Issue - State: open - Opened by OceaneMion 9 months ago - 8 comments

#74 - Segmeth identification of 5mC at CG motif

Issue - State: closed - Opened by JuandeBarba 9 months ago - 3 comments

#72 - Methylartist composite: Too few calls on seg

Issue - State: open - Opened by NinoPandiloski 11 months ago

#71 - wgmeth: AttributeError: 'NoneType' object has no attribute 'split'

Issue - State: open - Opened by J35P312 almost 1 year ago - 3 comments

#70 - segplot x-axis limit?

Issue - State: closed - Opened by itslittman about 1 year ago - 3 comments

#69 - BAM file checking

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

#68 - RNA modbams?

Issue - State: open - Opened by itslittman about 1 year ago - 2 comments

#67 - EDIT: new install throws keyError but old one works

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

#66 - segmeth error .

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

#65 - `--skip_align_plot` doesn't work

Issue - State: open - Opened by PanZiwei about 1 year ago - 2 comments

#64 - Question about the parameters of `methylartist locus`

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

#63 - Invalid script entry point when installing `methylartist==1.2.8`

Issue - State: closed - Opened by PanZiwei about 1 year ago - 3 comments

#62 - Fields in the Segmeth tsv output

Issue - State: open - Opened by vyx-lucy-kaplun about 1 year ago

#61 - Segmentation Fault Error

Issue - State: open - Opened by rekharichardson1 about 1 year ago - 2 comments

#60 - Error violin plots

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

#59 - syntax error when running methylartist

Issue - State: closed - Opened by stooz5 over 1 year ago - 3 comments

#58 - Is it possible to output the smoothed methylation fraction data?

Issue - State: open - Opened by weishwu over 1 year ago - 4 comments
Labels: enhancement

#57 - Issue with bam files from guppy

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

#56 - issue with split_on_adapter output

Issue - State: open - Opened by itslittman over 1 year ago - 2 comments

#55 - Issues with Bam files from Dorado with segmeth

Issue - State: open - Opened by Jared-Tomei over 1 year ago - 2 comments

#54 - Modified-Base calling of pod5 files with Dorado, what's next ?

Issue - State: closed - Opened by 120985 over 1 year ago - 3 comments

#53 - Segmeth killed

Issue - State: open - Opened by SophiaNavis20 over 1 year ago

#52 - mm10 genome

Issue - State: closed - Opened by srkndgn over 1 year ago - 5 comments

#51 - NameError: name 'b' is not defined

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

#50 - Segmeth error "IndexError: list index out of range"

Issue - State: open - Opened by sonalhenson over 1 year ago - 2 comments

#49 - Segmeth annotation bed file

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

#47 - motif

Issue - State: closed - Opened by duhuipeng over 1 year ago - 5 comments

#46 - Mismatch between locus and region

Issue - State: open - Opened by Violeta-de-Anca over 1 year ago - 2 comments

#45 - genome to CpG plot on methylartist locus

Issue - State: open - Opened by Chlo21030409 over 1 year ago - 1 comment

#44 - question with installation

Issue - State: open - Opened by rl4940 almost 2 years ago - 3 comments

#43 - Some problems About Gtf

Issue - State: closed - Opened by luoqh17 almost 2 years ago - 3 comments
Labels: enhancement

#42 - Bam file from PromethION as input?

Issue - State: open - Opened by CWYuan08 almost 2 years ago - 7 comments

#41 - output file / path name

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

#40 - Custom sample colors in -b mode

Issue - State: closed - Opened by yuliamostovoy almost 2 years ago - 3 comments
Labels: documentation, enhancement

#39 - Using a large BAI or CSI Index with Composite Function

Issue - State: closed - Opened by pgrady1322 almost 2 years ago - 3 comments
Labels: bug

#38 - Use of Guppy after version 1.2.6

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

#37 - log probability ratio shadow lines

Issue - State: open - Opened by Chlo21030409 about 2 years ago - 1 comment

#36 - adding multiple coordinate

Issue - State: closed - Opened by Fatihlrcfs about 2 years ago

#35 - Unclear scoredist plot with modbam input

Issue - State: open - Opened by weilu1998 about 2 years ago

#34 - Seaborn package version check

Issue - State: closed - Opened by Iamyuchiii about 2 years ago - 1 comment

#33 - Plot of aggregate profile over genes with flanking regions

Issue - State: open - Opened by yusmiatiliau about 2 years ago
Labels: enhancement

#31 - NoMe-Seq data

Issue - State: open - Opened by vivekbhr about 2 years ago - 6 comments

#30 - Methylartist wgmeth - IndexError: list index out of range

Issue - State: open - Opened by jo-ong about 2 years ago - 18 comments

#29 - fast5 does not seem to contain basecalling information

Issue - State: closed - Opened by Fatihlrcfs over 2 years ago - 19 comments

#28 - bam files from nanopore RRMS data and Methylbed file for methylartist

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

#27 - About sorting the GTF file

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

#26 - methylartist locus y-axis

Issue - State: closed - Opened by partha434 over 2 years ago - 3 comments
Labels: enhancement

#25 - .bam extension required for -b option to methylartist regions

Issue - State: closed - Opened by lfearnley over 2 years ago - 2 comments
Labels: documentation, enhancement

#23 - ValueError: Could not interpret value `coord` for parameter `x`

Issue - State: closed - Opened by raquelgarza over 2 years ago - 17 comments
Labels: enhancement

#22 - motif name CHG, CHH for normalizing window sizes

Issue - State: open - Opened by gaushi over 2 years ago - 3 comments
Labels: enhancement

#21 - Locus "insufficient coverage for plot" with modbam

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

#20 - modbam input ?

Issue - State: closed - Opened by colindaven over 2 years ago - 1 comment

#18 - local variable 'mm' referenced before assignment

Issue - State: closed - Opened by FraHaa21 over 2 years ago - 7 comments

#17 - Issue setting height ratios with methylartist locus

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

#16 - Does methylartist work with bedMethyl?

Issue - State: closed - Opened by YingziZhang-github over 2 years ago - 2 comments

#15 - ValueError: Could not interpret input 'sample'

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

#14 - blank result from segplot

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

#13 - segmeth output/running time

Issue - State: closed - Opened by Coracollar almost 3 years ago - 7 comments

#12 - megalodon-db sqlite3.OperationalError: disk I/O error

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

#11 - Error running segmeth command

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

#10 - .db files, annotation and multiple files.

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

#9 - Change the position of the sample name

Issue - State: closed - Opened by njaupan almost 3 years ago - 2 comments

#8 - How to import multi-files？

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

#7 - segmeth - not enoug values to unpack

Issue - State: closed - Opened by 0Bernhard about 3 years ago - 1 comment

#6 - Error when running segmeth Value error: invalid contig

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

#5 - Read mappings not showing up

Issue - State: closed - Opened by cstill3928 over 3 years ago - 4 comments

#4 - Smoothed methylation fraction color question

Issue - State: closed - Opened by cstill3928 over 3 years ago - 2 comments

#3 - --phased option for methylartist region

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

#2 - Full set of dependencies not installing?

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

#1 - A few bugs

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