yarden/miso issues and pull requests

#151 - RuntimeWarning: Long {deleted, inserted} alignment

Issue - State: open - Opened by jma1991 about 1 month ago

#150 - How to determine that a variable clipping event is a difference variable clipping event?

Issue - State: open - Opened by happypiggyzjx 2 months ago

#149 - Error on Smart-seq paired-end data

Issue - State: open - Opened by HZT55 5 months ago

#148 - Misopy didn't work with pickle and gave an error on the file Gene.py

Issue - State: open - Opened by mlcsmits 6 months ago

#147 - Installing and running miso

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

#146 - install error and plot error

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

#145 - Update all the dead genes.mit.edu links in the documentation page

Pull Request - State: open - Opened by KidElectric almost 2 years ago

#144 - different maximum values of y-axis for different samples in one plot

Issue - State: closed - Opened by Seanduu almost 2 years ago

#143 - Alternative Splicing Events annotations download link is erro

Issue - State: open - Opened by ChristopherLeeZG about 3 years ago - 2 comments

#142 - ValueError: too many values to unpack

Issue - State: open - Opened by husamia over 3 years ago

#141 - which part should I modify?

Issue - State: open - Opened by weifei888 almost 4 years ago

#140 - index_gff killed with no explanation

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

#139 - annotation file links not working

Issue - State: closed - Opened by KunFang93 over 4 years ago - 1 comment

#138 - Update sashimi.rst

Pull Request - State: open - Opened by jrobinso about 5 years ago

#137 - No events captured during compare differential isoforms

Issue - State: open - Opened by Sealzad about 5 years ago

#136 - import pysplicing

Issue - State: open - Opened by MurliNair over 5 years ago - 5 comments

#135 - Only works with samtools <= 1.2

Issue - State: open - Opened by pcarbo over 5 years ago

#134 - Unstable running results.

Issue - State: open - Opened by tangxj98 over 5 years ago

#133 - ValueError: numpy.dtype has the wrong size, try recompiling. Expected 88, got 96

Issue - State: open - Opened by sneha100895 over 5 years ago - 1 comment

#132 - RuntimeWarning: Long deleted alignment at pysplicing/src/solve.c:281

Issue - State: open - Opened by zhengjiantao over 5 years ago - 1 comment

#131 - RuntimeWarning

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

#130 - About testing error

Issue - State: open - Opened by zhengjiantao almost 6 years ago - 1 comment

#129 - sam_utils.py problem

Issue - State: open - Opened by obenno almost 6 years ago

#128 - Installation error: setting file does not exist

Issue - State: open - Opened by giuseppedelnapalle almost 6 years ago

#127 - The Python Apocalypse leads to Documentation Bug

Issue - State: open - Opened by lachlansimpson about 6 years ago

#126 - Queries related to Bayes factor, Exon Co-ordinates

Issue - State: open - Opened by sarath-omics about 6 years ago

#125 - How to get SAM file?

Issue - State: open - Opened by werhoog about 6 years ago

#124 - version 0.5.4 vs 0.5.2

Issue - State: open - Opened by mcbenkface about 6 years ago - 1 comment

#123 - Alternative Splicing Events annotations for GRCh38.

Issue - State: open - Opened by edkonyakhina about 6 years ago - 3 comments

#122 - MISO Output error

Issue - State: open - Opened by ibmuller about 6 years ago - 1 comment

#121 - Fix custom plot label option with filenames

Pull Request - State: open - Opened by trevortknguyen over 6 years ago

#120 - how to interpret the miso_posterior_mean

Issue - State: open - Opened by yiyimanew over 6 years ago

#119 - pip install issues

Issue - State: open - Opened by fu over 6 years ago

#118 - Problems with mpl_toolkits.axes_grid

Issue - State: open - Opened by pedropenzuti over 6 years ago - 1 comment

#117 - IndexError: too many indices for array

Issue - State: open - Opened by limeng12 over 6 years ago - 4 comments

#116 - Bug fix for sashimi_plot with --plot-label option

Issue - State: open - Opened by tdanhorn over 6 years ago - 2 comments

#115 - Error generating custom exon-centric annotations

Issue - State: closed - Opened by dejonggr almost 7 years ago

#114 - sashimi_plot with index_gff --compressed-id parameter

Issue - State: open - Opened by genetalks-fred almost 7 years ago

#113 - Fixed crashing on alignment files without sequence data

Pull Request - State: open - Opened by romansloutsky about 7 years ago - 1 comment

#112 - check_gff_and_bam() fails when BAM file does not contain read sequences

Issue - State: open - Opened by romansloutsky about 7 years ago

#111 - fixing samtools sort output

Pull Request - State: open - Opened by baileyglen about 7 years ago - 2 comments

#110 - Download link does not work

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

#109 - summarize_miso error

Issue - State: closed - Opened by wxzheng001 about 7 years ago

#108 - Python.h does not exist on pip install misopy

Issue - State: open - Opened by AMChalkie about 7 years ago - 2 comments

#107 - Can't use the most recent version of samtools

Issue - State: open - Opened by MITiGEM2017 about 7 years ago - 2 comments

#106 - Colons in job file name causing problems with SGE qsub

Issue - State: open - Opened by sepidehparhami about 7 years ago - 1 comment

#105 - Issue parsing queue job id

Issue - State: open - Opened by sepidehparhami about 7 years ago - 1 comment

#104 - settings.txt does not exist

Issue - State: open - Opened by royfrancis about 7 years ago - 5 comments

#103 - Bug in credible_intervals.py

Issue - State: closed - Opened by jano15 over 7 years ago - 5 comments

#102 - index_gff take very long time

Issue - State: closed - Opened by jano15 over 7 years ago

#101 - Extraction of splicing events from user speficied gene annotation (gtf or gff)

Issue - State: closed - Opened by akesarwani over 7 years ago - 1 comment

#100 - MISO, new update ?

Issue - State: open - Opened by lmanchon over 7 years ago

#99 - Update sashimi.rst

Pull Request - State: open - Opened by kerkomen over 7 years ago

#98 - IndexError when summarizing and comparing MISO results

Issue - State: closed - Opened by althornt over 7 years ago - 8 comments

#97 - Status of conda package?

Issue - State: open - Opened by holtgrewe over 7 years ago - 2 comments

#96 - Batch-logs file not being created

Issue - State: open - Opened by hershbc over 7 years ago - 2 comments

#95 - Error: need --output-dir to compute Psi values.

Issue - State: closed - Opened by pillailab almost 8 years ago - 1 comment

#94 - Variable Read Length

Issue - State: open - Opened by dlukacso almost 8 years ago

#93 - TypeError

Issue - State: open - Opened by lpipes almost 8 years ago

#92 - Best-guessing insert size and stddev using paired-end data versus running miso single ended

Issue - State: open - Opened by fpbarthel about 8 years ago - 2 comments

#91 - MISO test run failed !

Issue - State: open - Opened by ya73 about 8 years ago - 5 comments

#90 - Parse command string

Pull Request - State: open - Opened by dlsrnsi about 8 years ago - 1 comment

#89 - All isoforms shorter than read length 150,always skipping

Issue - State: closed - Opened by john321123 about 8 years ago

#88 - Slurm support

Pull Request - State: open - Opened by aaronk over 8 years ago - 1 comment

#87 - Adjust Max y-axis for sashimi_plot

Issue - State: open - Opened by cfbuenabadn over 8 years ago

#86 - Slurm support

Issue - State: open - Opened by aaronk over 8 years ago - 20 comments

#85 - Update setup.py

Pull Request - State: closed - Opened by aaronk over 8 years ago - 5 comments

#84 - How are indels, soft-clipping in CIGAR handled? Affected by read length?

Issue - State: open - Opened by SolKatzman over 8 years ago

#83 - Compiling fastmiso on mac (can't find 'miso' / 'index_gff' / 'sashami_plot' executables)

Issue - State: closed - Opened by cwarden45 over 8 years ago - 1 comment

#82 - strand_rule error

Issue - State: closed - Opened by dauss75 over 8 years ago - 1 comment

#81 - Does the insert length mean fragment length?

Issue - State: closed - Opened by huangyh09 over 8 years ago - 2 comments

#80 - Issue with psi values in miso files

Issue - State: open - Opened by ryanabo almost 9 years ago - 2 comments

#79 - Fix misnamed logger variable

Pull Request - State: closed - Opened by jrbotros about 9 years ago - 1 comment

#78 - fix import statement setup.py, required because entry_points is used

Pull Request - State: closed - Opened by boegel over 9 years ago - 6 comments

#77 - Pairedbug

Pull Request - State: closed - Opened by gaborcsardi over 9 years ago - 1 comment

#76 - unpack miso output for sashimi_plot

Issue - State: open - Opened by pengchy over 9 years ago - 8 comments

#75 - running multiple miso jobs ( one per sample ) independently using an index, fails as shelves are not built for concurrent reads

Issue - State: open - Opened by xshah over 9 years ago - 9 comments

#74 - changelog

Issue - State: closed - Opened by olgabot over 9 years ago - 1 comment

#73 - Use Travis CI

Issue - State: closed - Opened by yarden over 9 years ago - 7 comments

#72 - License unclear

Issue - State: closed - Opened by rekado over 9 years ago - 1 comment

#71 - building with python 3 fails

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

#70 - spawned python processes

Issue - State: open - Opened by ink1 almost 10 years ago - 1 comment

#69 - Cannot load misopy after installing to staged python 2.7 location using pip

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

#68 - Error on provided drosophila annotations

Issue - State: open - Opened by ohadgl almost 10 years ago

#67 - MISO on MAC 10.9: malloc error

Issue - State: open - Opened by Jerry-Zhao over 10 years ago - 5 comments

#66 - run_SGEarray_cluster() throws error in SGE-6.0u8. Possibly qsub priority bug.

Issue - State: open - Opened by jakeyeung over 10 years ago

#65 - annotation file

Issue - State: open - Opened by nickytong over 10 years ago

#64 - log_score = nan?

Issue - State: open - Opened by olgabot over 10 years ago - 8 comments

#63 - Reproducibility of Miso results

Issue - State: open - Opened by robcarr over 10 years ago - 1 comment

#62 - Reads thrown out?

Issue - State: open - Opened by olgabot over 10 years ago - 5 comments

#61 - Creating new AS annotation

Issue - State: closed - Opened by ramaniak almost 11 years ago - 1 comment

#60 - Properly paired on tophat output

Issue - State: closed - Opened by frontal almost 11 years ago - 3 comments

#59 - Add python shebang to the top

Pull Request - State: open - Opened by roryk almost 11 years ago - 10 comments

#58 - Creating my own gff3 file

Issue - State: closed - Opened by frontal almost 11 years ago - 1 comment

#57 - No query here. solved by myselft :) can be deleted

Issue - State: closed - Opened by frontal almost 11 years ago

#56 - Problem with assigned_counts

Issue - State: closed - Opened by mnsmar almost 11 years ago - 3 comments

#55 - GFF IDs don't correspond to exon start/stops

Issue - State: open - Opened by olgabot about 11 years ago - 2 comments

#54 - Add `which_miso`

Issue - State: open - Opened by yarden about 11 years ago

#53 - Error checking for tagBam

Issue - State: open - Opened by yarden about 11 years ago

#52 - Fix Python version path issue

Issue - State: closed - Opened by yarden about 11 years ago

GitHub / yarden/miso issues and pull requests