YeoLab outrigger issues

YeoLab / outrigger

Create a *de novo* alternative splicing database, validate splicing events, and quantify percent spliced-in (Psi) from RNA seq data

http://yeolab.github.io/outrigger/

BSD 3-Clause "New" or "Revised" License

62 stars 22 forks source link

issues

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outrigger --index error: "AttributeError: 'Series' object has no attribute 'iteritems'"

#104 jordimaggi opened 1 year ago
1
sqlite3.OperationalError: disk I/O error

#103 LiangShaw opened 3 years ago
0
ValueError: Cannot mask with non-boolean array containing NA / NaN values error

#102 titand98 opened 3 years ago
0
how to set multiple threads

#101 fuhao1216 opened 3 years ago
0
Database locked when detecting de novo exons after no novel exons found on a chromosome

#100 QuentinLetourneur opened 4 years ago
0
ImportError: libcrypto.so.1.0.0: cannot open shared object file: No such file or directory

#99 dwooi closed 4 years ago
0
KeyError: junction

#98 wbvguo opened 4 years ago
2
Distinguish last_read_pos == 0 and last_read_pos is None

#97 gokceneraslan closed 4 years ago
1
Calculating PSI of single-cell data with outrigger

#96 hmutpw opened 4 years ago
1
Unstacked DataFrame is too big, causing int32 overflow

#95 Qi-Yang-Bioinfo opened 4 years ago
0
How to use outrigger index with "-c"?

#94 QijinYin opened 4 years ago
0
NotImplementedError: "flankBed"

#93 YutingMa68 opened 5 years ago
0
Confusions about the contents of events.csv

#92 mouni521 closed 4 years ago
0
How to set the "--n-jobs" parameter?

#91 ttchuanbao closed 6 years ago
0
RI events

#90 limeng12 closed 4 years ago
2
Table 'GRCh37.chromInfo' doesn't exist // ERROR: chrom "14" not found in genome file. Exiting.

#89 Ekomshiro opened 6 years ago
4
ERROR IN -- Creating a "gffutils" database ---"database is locked"

#88 memooooooo opened 7 years ago
0
Core error when running outriger psi

#87 cfbuenabadn opened 7 years ago
0
New release: v1.1.0rc1

#86 olgabot closed 7 years ago
0
conda env create

#85 mlovci opened 7 years ago
5
outrigger index looping forever while updating gffutils database with novel exons on chr10 (mm10)

#84 alaindomissy opened 7 years ago
0
outrigger index fails processing bam files with UnboundLocalError: local variable 'start' referenced before assignment

#83 alaindomissy closed 4 years ago
10
outrigger validate fails when outrigger_output/index/mxe/exon1.bed does not exist

#82 ghost opened 7 years ago
2
outrigger index --splice-types error - KeyError: 'mxe'

#81 ghost opened 7 years ago
1
outrigger index is dying

#80 ecwheele closed 7 years ago
3
Remember, flat is better than nested

#79 olgabot opened 7 years ago
1
Be explicit about inputs/outputs

#78 olgabot opened 7 years ago
0
Update Documentation

#77 olgabot opened 7 years ago
0
Logo

#76 olgabot closed 7 years ago
0
Py3.6

#75 olgabot closed 7 years ago
0
Checklist

#74 olgabot closed 7 years ago
0
coveralls.io leaks your information

#73 aviaoh closed 7 years ago
1
Concatenate `psi/se/summary.csv` and `psi/mxe/summary.csv`

#72 olgabot opened 7 years ago
0
Add link to Slack's empathy in pull requests link to `PULL_REQUEST` template

#71 olgabot opened 7 years ago
0
Remove features with exon lengths==1

#70 olgabot opened 7 years ago
0
UNIQUE id error on tasic2016_big dataset

#69 olgabot closed 7 years ago
2
Installing via `environment.yml` doesn't add command line entry points

#68 olgabot opened 7 years ago
2
Case Xa/b doesn't show - only "Case Xa"

#67 olgabot opened 7 years ago
0
If novel_exons.gtf exists, still gets overwritten

#66 olgabot opened 7 years ago
0
When using an external junction reads file, copy to `outrigger_output` folder

#65 olgabot opened 7 years ago
0
Segmentation fault on large datasets

#64 olgabot opened 7 years ago
1
v1.0.0rc1 - Version 1.0.0, release candidate 1

#63 olgabot closed 7 years ago
8
Add co-splicing metric for retained introns

#62 olgabot opened 8 years ago
0
WIP: Fix logic

#61 olgabot closed 7 years ago
0
Add GitHub link in README for redirect from PyPI

#60 willingc opened 8 years ago
0
Add Documentation

#59 olgabot closed 7 years ago
2
Deal with insufficient read depth cases well

#58 olgabot closed 7 years ago
0
Low memory

#57 olgabot closed 8 years ago
2
Flake8 weirdness

#56 olgabot closed 8 years ago
1
Add conda environment for dev

#55 willingc closed 8 years ago
7