Ecosyste.ms: Issues

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GitHub / Xinglab/rmats2sashimiplot issues and pull requests

#137 - Clarification on Exon Inclusion Representation in Visualizations

Issue - State: open - Opened by COOL005 7 days ago - 3 comments

#136 - errors with 'mpl_toolkits.axes_grid'

Issue - State: closed - Opened by Angelia111 about 2 months ago - 1 comment

#135 - Rmats image

Issue - State: open - Opened by alquamalok22 about 2 months ago - 1 comment

#133 - Potential bugs in the rmats2sashimiplot visualization

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

#132 - Package installation

Issue - State: closed - Opened by Yuqiu-Yang 6 months ago - 2 comments

#131 - rMATS-long and rmats2sashimiplot

Issue - State: open - Opened by suiyue7 6 months ago - 1 comment

#130 - Error checking bam files

Issue - State: open - Opened by RaghdaKailany 6 months ago - 1 comment

#129 - Analyzing pair analysis data

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

#127 - 2to3.sh not working

Issue - State: open - Opened by AleixPalahi 7 months ago - 1 comment

#126 - RPKM values as output instead of the sashimiplot pdf

Issue - State: closed - Opened by mlcsmits 7 months ago - 4 comments

#125 - Filter average 0 junction read on the plot

Issue - State: open - Opened by Qingru44004 7 months ago - 1 comment

#124 - sashimi group

Issue - State: open - Opened by Qingru44004 7 months ago - 3 comments

#123 - rmats2sashimiplot didn't create the PDF file with the plot

Issue - State: closed - Opened by mlcsmits 8 months ago - 4 comments

#122 - Separate label for each sample in `--b1`

Issue - State: open - Opened by dmgie 9 months ago

#121 - problem in using grouping option and coordinates?

Issue - State: closed - Opened by edonato28 9 months ago - 4 comments

#120 - Help to understand group sashimi plot

Issue - State: open - Opened by Sahu-Mousumi 9 months ago - 1 comment

#119 - Help with rmats2sashimiplot

Issue - State: open - Opened by Sahu-Mousumi 10 months ago - 1 comment

#118 - Is there a problem providing sorted bam files to rMATS?

Issue - State: open - Opened by Sahu-Mousumi 10 months ago - 1 comment

#116 - 'nan' in sashimiplot PDF file

Issue - State: open - Opened by bioPG 11 months ago - 4 comments

#115 - ValueError: 'chr' is not in list

Issue - State: open - Opened by Portulaca666 12 months ago - 1 comment

#113 - IOError: truncated file

Issue - State: open - Opened by deb0612 12 months ago - 3 comments

#111 - About RPKM

Issue - State: open - Opened by ESWRKJ 12 months ago - 1 comment
Labels: duplicate

#110 - First/Last sample in each grouping always return nan

Issue - State: open - Opened by EspressoKris about 1 year ago - 4 comments

#109 - Add WDL

Pull Request - State: closed - Opened by EricKutschera about 1 year ago - 1 comment

#108 - WDL script for rmats2sashimiplot

Issue - State: closed - Opened by JingAnyaSun about 1 year ago - 2 comments

#106 - Update to version 3.0.0

Pull Request - State: closed - Opened by EricKutschera about 1 year ago

#105 - Add Dockerfile

Pull Request - State: closed - Opened by EricKutschera about 1 year ago

#104 - Install the master version of rmats2sashimiplot by conda

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

#103 - Replace deprecated matplotlib import

Pull Request - State: closed - Opened by EricKutschera over 1 year ago

#101 - About BAM file error

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

#100 - What is the exception in the `plot_with_eventsfile`

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

#99 - How to understand the content in plot of rmats2sashimiplot?

Issue - State: closed - Opened by CarrieBishop over 1 year ago - 4 comments

#98 - fetch called on bamfile without index

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

#96 - ModuleNotFoundError: No module named 'pysam'

Issue - State: closed - Opened by CarrieBishop over 1 year ago - 9 comments

#95 - error while running on test data

Issue - State: closed - Opened by rezarahman12 over 1 year ago - 8 comments

#94 - after running,no plot file

Issue - State: closed - Opened by 44314474 over 1 year ago - 2 comments

#93 - Parse --min-counts as an int

Pull Request - State: closed - Opened by EricKutschera over 1 year ago

#92 - Issue with gff3 file

Issue - State: closed - Opened by Oliverfeudj over 1 year ago - 10 comments

#91 - Data type error of --min-counts

Issue - State: closed - Opened by wu116 over 1 year ago - 1 comment

#90 - Missing required python packages: scipy and pysam

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

#89 - Region cannot be stored in bai index

Issue - State: closed - Opened by seandris almost 2 years ago - 1 comment

#88 - Allow s1,s2,b1,b2 arguments to be a file containing paths

Pull Request - State: closed - Opened by EricKutschera almost 2 years ago

#87 - IndexError: list index out of range

Issue - State: closed - Opened by deb0612 almost 2 years ago - 3 comments

#86 - Rmats2sashimiplot error

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

#85 - low quantity of fpkm in sashimi plot

Issue - State: closed - Opened by ElenaSLuis about 2 years ago - 3 comments

#84 - sample_labels = NA

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

#83 - SyntaxError: Missing parentheses in call to 'print'

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

#82 - Empty gff file

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

#81 - Adjust subplot width depending if to plot posterior distributions

Pull Request - State: closed - Opened by ycl6 over 2 years ago

#80 - Add options to adjust figure size

Pull Request - State: closed - Opened by ycl6 over 2 years ago

#79 - sashimi does not match IncLevel

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

#78 - IndexError

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

#77 - IndexError: list index out of range

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

#76 - Update isoform coordinates

Pull Request - State: closed - Opened by EricKutschera almost 3 years ago

#75 - Sashimi plot not generated

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

#74 - Figure not generated

Issue - State: closed - Opened by ShenTTT about 3 years ago

#73 - Large number of samples not supported?

Issue - State: closed - Opened by OnkarMulay about 3 years ago - 2 comments

#72 - 'chr' is not in list error

Issue - State: closed - Opened by dhivyaa-6 about 3 years ago - 4 comments

#71 - IndexError: list index out of range

Issue - State: closed - Opened by OnkarMulay about 3 years ago - 21 comments

#70 - Should rmats2sashimiplot use FPKM and not RPKM for paired end analysis?

Issue - State: open - Opened by gtollefson about 3 years ago - 1 comment
Labels: enhancement

#69 - Some sashimiplots are unlike the corresponding events found by rmats

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

#68 - Result interpretation

Issue - State: closed - Opened by elva0328 about 3 years ago - 4 comments

#67 - Add options to control removal of 'chr' from events file

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#66 - Conditionally require a label argument

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#65 - Using rmats2sashimiplot with just one group

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

#64 - Invalid Contig

Issue - State: closed - Opened by atly2000 over 3 years ago - 5 comments

#63 - Replace ':' with '_'

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#62 - rmats2sashimiplot: error: argument --exon_s: invalid int value: './SE.MATS.JC.txt'

Issue - State: closed - Opened by sr8510 over 3 years ago - 7 comments

#61 - can‘t find pdf files

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

#60 - How to restrict the splicing analysis to events with 10 or more reads?

Issue - State: closed - Opened by elva0328 over 3 years ago - 4 comments

#59 - Allow using a csi index for bam files

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#58 - Bam file indexing error

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

#57 - missing junction on a plot

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

#56 - Update package files for v2.0.4

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#55 - Use pysam instead of samtools to process the first alignment

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#54 - Update rmats2sashimiplot.py

Pull Request - State: closed - Opened by t-arae over 3 years ago - 2 comments

#53 - Update README FAQs

Pull Request - State: closed - Opened by EricKutschera over 3 years ago

#52 - color feature

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

#51 - invalid syntax

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

#50 - IndexError: index out of bounds

Issue - State: closed - Opened by shum-sky almost 4 years ago - 2 comments

#49 - query length in RPKM

Issue - State: closed - Opened by wangjiawen2013 almost 4 years ago - 1 comment

#47 - Plotting only specific genes

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

#45 - not working at all

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

#44 - Multiple threads

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

#43 - plot with one sample

Issue - State: closed - Opened by zpliu1126 over 4 years ago - 2 comments

#42 - Require only s1 or b1

Pull Request - State: closed - Opened by EricKutschera over 4 years ago - 1 comment

#41 - Update the README

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

#40 - RPKM values are in double digits or less. What am I doing wrong?

Issue - State: closed - Opened by mranjan1 over 4 years ago - 4 comments

#39 - Allow running with Python 3

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

#38 - Update warning and error messages

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