Ecosyste.ms: Issues

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GitHub / yarden/miso issues and pull requests

#49 - hi yarden

Issue - State: closed - Opened by charlesylin over 11 years ago - 1 comment

#48 - Fix `miso_zip.py` for Ensembl style chromosomes

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

#46 - Difficulty with malloc error

Issue - State: open - Opened by rahulcdeo over 11 years ago - 4 comments

#45 - Handle biological replicates automatically

Issue - State: open - Opened by roryk over 11 years ago - 4 comments

#44 - Add note on how to install python packages

Issue - State: closed - Opened by yarden over 11 years ago
Labels: Installation

#43 - Handle BAM files with unaligned reads

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

#42 - Implement --lazy for MAP estimate

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

#41 - Add --min-junctions argument to Sashimi plot

Issue - State: closed - Opened by yarden over 11 years ago
Labels: sashimi_plot

#40 - Add color schemes to sashimi_plot

Issue - State: open - Opened by yarden over 11 years ago
Labels: sashimi_plot

#39 - Fix up RPKM labels and align Psi tracks

Issue - State: open - Opened by yarden over 11 years ago
Labels: sashimi_plot

#38 - Switch to Ryan Dale's gffutils

Issue - State: open - Opened by yarden over 11 years ago
Labels: GFF

#37 - Reorganize GFF annotations, add new ones

Issue - State: open - Opened by yarden over 11 years ago
Labels: GFF, Annotation

#36 - Sanitize and annotate GFF files

Issue - State: open - Opened by yarden over 11 years ago
Labels: GFF, Annotation

#35 - Allow mixed iterations number comparisons

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

#34 - Convert all parsing from GFF3 to GTF

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

#33 - Detecting low or unrepresented transcripts

Issue - State: closed - Opened by alig99 over 11 years ago - 6 comments

#32 - Can Miso compare more than one mutant with a Wild type

Issue - State: closed - Opened by alig99 over 11 years ago - 1 comment

#31 - misopy not finding paired mates from Tophat Bam

Issue - State: closed - Opened by alig99 over 11 years ago - 3 comments

#30 - Eliminate delta posteriors output

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

#29 - Eliminate all scipy code from code base

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

#28 - Check for presence of BAM index

Issue - State: closed - Opened by yarden almost 12 years ago

#27 - BAM versus GFF header diagnostic tool

Issue - State: closed - Opened by yarden almost 12 years ago

#26 - Create compressed output for MISO

Issue - State: closed - Opened by yarden almost 12 years ago - 1 comment

#24 - Pre-filter reads (with bedtoools) to select events to run on

Issue - State: closed - Opened by yarden almost 12 years ago

#23 - Make MISO output a list of job IDs when using "--use-cluster"

Issue - State: open - Opened by yarden about 12 years ago

#22 - added support for virtualenv based installs

Pull Request - State: open - Opened by mbreese about 12 years ago - 1 comment

#21 - SGE/virtualenv compatability fixes, fixes to sashimi_plot for headless mode

Pull Request - State: closed - Opened by ericsuh over 12 years ago

#20 - Fixed permissions issue with SGE job submission script

Pull Request - State: closed - Opened by ericsuh over 12 years ago - 2 comments

#19 - Replicate on samples

Issue - State: closed - Opened by marcowanger over 12 years ago - 2 comments

#18 - What mapper does MISO supports?

Issue - State: closed - Opened by marcowanger over 12 years ago - 6 comments

#17 - Sashimi plot Error: need --output-dir

Issue - State: closed - Opened by marcowanger over 12 years ago - 3 comments

#16 - Better CIGAR string support

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 1 comment

#15 - BAM reader mixes up the TLEN field

Issue - State: open - Opened by gaborcsardi about 13 years ago

#14 - Dev

Pull Request - State: closed - Opened by mlovci about 13 years ago

#13 - More flexible BAM reader

Issue - State: open - Opened by gaborcsardi about 13 years ago - 1 comment

#12 - Variable read length

Issue - State: open - Opened by gaborcsardi about 13 years ago - 3 comments

#11 - Calculate fragment length from the data

Issue - State: closed - Opened by gaborcsardi about 13 years ago

#10 - Some framework to test the Python package

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 1 comment

#9 - Filtering function

Issue - State: open - Opened by gaborcsardi about 13 years ago

#8 - Run MCMC until convergence, instead of a fixed number of steps

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 2 comments

#7 - Order the GFF file, don't assume it was ordered, in the C code.

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 1 comment

#6 - Test Python RNG in the C code.

Issue - State: open - Opened by gaborcsardi about 13 years ago

#5 - Support overhang length in the C code.

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 2 comments

#4 - Use fragment length correctly in the C solver.

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 1 comment

#3 - Convert GFF to Python object.

Issue - State: closed - Opened by gaborcsardi about 13 years ago - 3 comments

#2 - "python" to sys.executable

Pull Request - State: closed - Opened by cassj about 13 years ago - 1 comment

#1 - added SGE array support

Pull Request - State: closed - Opened by mlovci about 13 years ago