Ecosyste.ms: Issues

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GitHub / Xinglab/rmats2sashimiplot issues and pull requests

#144 - add pip install description

Pull Request - State: closed - Opened by abearab 29 days ago - 2 comments

#143 - Check each bam file for an existing index file

Pull Request - State: closed - Opened by EricKutschera about 2 months ago - 1 comment

#142 - Incorrect Index Handling for Multiple BAM Files

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

#141 - Fix a FixedFormatter/FixedLocator warning (matplotlib)

Pull Request - State: closed - Opened by ycl6 2 months ago

#140 - To support gene symbols with special characters

Pull Request - State: closed - Opened by ycl6 2 months ago

#139 - Error when running on rMATS generated BAM files

Issue - State: open - Opened by nicholas-moskwa 3 months ago - 5 comments

#137 - Clarification on Exon Inclusion Representation in Visualizations

Issue - State: open - Opened by COOL005 4 months ago - 3 comments

#136 - errors with 'mpl_toolkits.axes_grid'

Issue - State: closed - Opened by Angelia111 5 months ago - 1 comment

#135 - Rmats image

Issue - State: open - Opened by alquamalok22 5 months ago - 1 comment

#133 - Potential bugs in the rmats2sashimiplot visualization

Issue - State: open - Opened by mumdark 6 months ago - 4 comments

#132 - Package installation

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

#131 - rMATS-long and rmats2sashimiplot

Issue - State: open - Opened by suiyue7 9 months ago - 1 comment

#130 - Error checking bam files

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

#129 - Analyzing pair analysis data

Issue - State: open - Opened by tanya-lasagne 10 months ago - 3 comments

#127 - 2to3.sh not working

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

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

Issue - State: closed - Opened by mlcsmits 11 months ago - 4 comments

#125 - Filter average 0 junction read on the plot

Issue - State: open - Opened by Qingru44004 11 months ago - 1 comment

#124 - sashimi group

Issue - State: open - Opened by Qingru44004 11 months ago - 3 comments

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

Issue - State: closed - Opened by mlcsmits 12 months ago - 4 comments

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

Issue - State: open - Opened by dmgie 12 months ago

#121 - problem in using grouping option and coordinates?

Issue - State: closed - Opened by edonato28 about 1 year ago - 4 comments

#120 - Help to understand group sashimi plot

Issue - State: open - Opened by Sahu-Mousumi about 1 year ago - 1 comment

#119 - Help with rmats2sashimiplot

Issue - State: open - Opened by Sahu-Mousumi about 1 year ago - 1 comment

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

Issue - State: open - Opened by Sahu-Mousumi about 1 year ago - 1 comment

#116 - 'nan' in sashimiplot PDF file

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

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

Issue - State: open - Opened by Portulaca666 about 1 year ago - 1 comment

#114 - Test example data: No entries found for gene chr16:9000:25001:+ in GFF

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

#113 - IOError: truncated file

Issue - State: open - Opened by deb0612 over 1 year ago - 3 comments

#111 - About RPKM

Issue - State: open - Opened by ESWRKJ over 1 year ago - 1 comment
Labels: duplicate

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

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

#109 - Add WDL

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

#108 - WDL script for rmats2sashimiplot

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

#106 - Update to version 3.0.0

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

#105 - Add Dockerfile

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

#104 - Install the master version of rmats2sashimiplot by conda

Issue - State: closed - Opened by bioPG over 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 almost 2 years ago - 9 comments

#95 - error while running on test data

Issue - State: closed - Opened by rezarahman12 almost 2 years ago - 8 comments

#94 - after running,no plot file

Issue - State: closed - Opened by 44314474 almost 2 years ago - 2 comments

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

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

#92 - Issue with gff3 file

Issue - State: closed - Opened by Oliverfeudj almost 2 years ago - 10 comments

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

Issue - State: closed - Opened by wu116 almost 2 years ago - 1 comment

#90 - Missing required python packages: scipy and pysam

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

#89 - Region cannot be stored in bai index

Issue - State: closed - Opened by seandris about 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 over 2 years ago

#87 - IndexError: list index out of range

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

#86 - Rmats2sashimiplot error

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

#85 - low quantity of fpkm in sashimi plot

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

#84 - sample_labels = NA

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

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

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

#82 - Empty gff file

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

#77 - IndexError: list index out of range

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

#76 - Update isoform coordinates

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

#75 - Sashimi plot not generated

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

#74 - Figure not generated

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

#73 - Large number of samples not supported?

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

#72 - 'chr' is not in list error

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

#71 - IndexError: list index out of range

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

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

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

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

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

#68 - Result interpretation

Issue - State: closed - Opened by elva0328 over 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 almost 4 years ago - 2 comments

#56 - Update package files for v2.0.4

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

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

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

#54 - Update rmats2sashimiplot.py

Pull Request - State: closed - Opened by t-arae almost 4 years ago - 2 comments

#53 - Update README FAQs

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

#52 - color feature

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

#51 - invalid syntax

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

#50 - IndexError: index out of bounds

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

#49 - query length in RPKM

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

#47 - Plotting only specific genes

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

#45 - not working at all

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