Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / GoekeLab/xpore issues and pull requests

#115 - Update __init.py__ to match 2.1

Pull Request - State: closed - Opened by matthewstuartedwards about 3 years ago - 1 comment

#114 - Are the initial data-prep steps now in line with m6anet?

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

#113 - add functions for tombo outputs

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

#110 - Errors while running xpore dataprep

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

#109 - ValueError: Expected object or value

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

#107 - Mixture of samples

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

#105 - update readthedocs with --gtf_or_gff specifics

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

#103 - Fix quickstart doc

Pull Request - State: closed - Opened by hendrikweisser over 3 years ago - 1 comment

#99 - Results Interpretation xPore 2.0

Issue - State: closed - Opened by Wardale24 over 3 years ago

#96 - add assert "NNNNN" for process_tx and solve bug with stringtie gtf

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

#94 - Feasibility of xpore to work on non-nanopore RNA-seq data

Issue - State: closed - Opened by ybfu88 over 3 years ago

#92 - DIffmod error

Issue - State: closed - Opened by Wardale24 over 3 years ago - 7 comments

#90 - Add GFF annotation option and change fasta and gtf input flags names

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

#89 - xpore dataprep error addition

Issue - State: closed - Opened by Wardale24 over 3 years ago - 3 comments

#88 - What happens when nanopolish model_kmer is NNNNN?

Issue - State: closed - Opened by cathoderaymission over 3 years ago - 2 comments
Labels: latest gitHub but not pypi yet

#87 - readGTF function was modified to adapt to non-ensembl GTF input

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

#86 - xpore dataprep empty data.json

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

#85 - readGTF split issue

Issue - State: closed - Opened by obenno over 3 years ago - 7 comments
Labels: latest gitHub but not pypi yet

#82 - add gff as annotation option in addition to gtf

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

#79 - Feature request: Report on methylation status of individual reads with location

Issue - State: open - Opened by cathoderaymission over 3 years ago
Labels: enhancement

#78 - Feature request: Process GFF files

Issue - State: closed - Opened by cathoderaymission over 3 years ago
Labels: enhancement

#76 - xpore diffmod module

Issue - State: closed - Opened by Lqh09 over 3 years ago

#74 - Positions in the result are 0-based?

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

#73 - xpore processing of Epinano Yeast fails

Issue - State: closed - Opened by cathoderaymission over 3 years ago - 10 comments

#72 - xpore v2.0 dataprep ERROR

Issue - State: closed - Opened by DrDaedalusWHU over 3 years ago - 10 comments
Labels: answered

#71 - When will the conda package be updated to 2.0?

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

#67 - Update help.rst

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

#66 - Update README.md

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

#65 - Prolems about long mRNA reads mapping

Issue - State: closed - Opened by lwlive over 3 years ago - 2 comments
Labels: answered

#59 - xpore MinION data access

Issue - State: closed - Opened by sumin5784 over 3 years ago - 2 comments

#57 - remove pyensembl requirement and solve Arabidopsis bug

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

#56 - remove pyensembl requirement only

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

#55 - Genome mapping for Arabidopsis in Xpore

Issue - State: closed - Opened by Annie-GW almost 4 years ago - 14 comments

#54 - xpore-diffmode error

Issue - State: closed - Opened by al3xMlt almost 4 years ago - 3 comments

#53 - xpore-diffmod hangs on error

Issue - State: closed - Opened by callumparr almost 4 years ago - 7 comments

#52 - qsub batch jobs

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

#51 - Update README.md

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

#50 - remove pyensembl requirement and add m6anet dataprep functions

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

#49 - Update README.md

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

#48 - gtf option, fastdataprep, and dataprep intermediate file removal

Pull Request - State: closed - Opened by yuukiiwa about 4 years ago

#47 - Download datasets

Issue - State: closed - Opened by q1134269149 about 4 years ago - 4 comments

#46 - Guppy software version for base calling

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

#45 - Diffmod error output but seems to run.

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

#43 - Typical run time and file size

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

#42 - Not found in index error

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

#40 - Last version not available from pypi

Issue - State: closed - Opened by a-slide about 4 years ago - 8 comments

#39 - keep tx_id without tx_version

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

#38 - run dataprep errors

Issue - State: closed - Opened by q1134269149 over 4 years ago - 5 comments

#34 - Option n_processes in xpore-dataprep

Issue - State: closed - Opened by lionelus over 4 years ago - 1 comment
Labels: info

#32 - Empty outputs from dataprep

Issue - State: closed - Opened by matthew-valentine over 4 years ago - 9 comments

#31 - xpore/xpore/diffmod/model_kmer.csv

Issue - State: closed - Opened by pa6774ac-s over 4 years ago - 2 comments
Labels: enhancement

#30 - results interpretation

Issue - State: closed - Opened by Huanle over 4 years ago - 8 comments
Labels: info

#29 - RNA sequence kit

Issue - State: closed - Opened by pabloacera over 4 years ago - 1 comment
Labels: info

#28 - weird struct.error when running xpore-diffmod

Issue - State: closed - Opened by pabloacera over 4 years ago - 2 comments
Labels: fixed

#21 - provide a GTF file for transcript to genome mapping

Issue - State: closed - Opened by mparker2 over 4 years ago - 1 comment
Labels: enhancement, fixed

#18 - Error with xpore-dataprep

Issue - State: closed - Opened by lingolingolin over 4 years ago - 16 comments
Labels: fixed

#16 - Make p_overlap as a user option

Issue - State: closed - Opened by ploy-np over 4 years ago

#15 - --save_models

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

#13 - Post-processing for prioritisation

Issue - State: closed - Opened by ploy-np over 4 years ago

#10 - eventaligned.hdf5

Issue - State: closed - Opened by ploy-np over 4 years ago

#5 - xpore/scripts/xpore-dataprep: steps

Issue - State: closed - Opened by ploy-np about 5 years ago - 3 comments

#4 - Installation of all dependencies

Issue - State: closed - Opened by ploy-np about 5 years ago - 2 comments