Ecosyste.ms: Issues

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

GitHub / tleonardi/nanocompore issues and pull requests

#230 - ref kmer and position of modification

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

#229 - Direction of change in methylation

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

#228 - sharkfin plot too many data points and difficult to visualize

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

#227 - Fixed numpy.float depreciated behaviour

Pull Request - State: open - Opened by lmulroney about 1 year ago

#225 - numpy' has no attribute 'float'.

Issue - State: closed - Opened by Rohit-Satyam about 1 year ago - 3 comments

#224 - db type is dbm.gnu, but the module is not available

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

#223 - Steps to make Nanocompore Work

Issue - State: closed - Opened by Rohit-Satyam over 1 year ago - 1 comment

#222 - Nanocompore SampComp stuck at 0%

Issue - State: open - Opened by sidizhao over 1 year ago - 8 comments

#221 - SystemError: null argument to internal routine

Issue - State: open - Opened by kwonej0617 over 1 year ago - 7 comments

#220 - Problems with save_to_bed. And questions with bed file annotation

Issue - State: closed - Opened by XqKang over 1 year ago - 1 comment

#219 - nanocompore sampcomp output question.

Issue - State: closed - Opened by fgfrost over 1 year ago - 5 comments

#218 - nanocompore-sampcomp-References found in index: 0

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

#217 - A question about the result

Issue - State: open - Opened by Tomcxf almost 2 years ago - 1 comment

#216 - miCLIP dataset

Issue - State: closed - Opened by kwonej0617 almost 2 years ago - 2 comments

#215 - Bump joblib from 0.17.0 to 1.1.1

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#214 - returns numpy error while intsalling nanocompore on Ubuntu 22.04

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

#213 - nanocompore to be used for SHAPEseq data

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

#211 - Issues on reproducing the synthetic oligo results from the nanocompore paper

Issue - State: closed - Opened by loganylchen almost 2 years ago - 3 comments

#210 - cluster_counts interpretation

Issue - State: closed - Opened by sunsetyerin about 2 years ago - 1 comment

#209 - plot position is giving an error

Issue - State: closed - Opened by Muhammad5577 about 2 years ago - 5 comments

#208 - dbm.error: db file doesn't exist; use 'c' or 'n' flag to create a new db

Issue - State: closed - Opened by sunsetyerin about 2 years ago - 21 comments

#207 - SampCompDB error

Issue - State: open - Opened by rezarahman12 over 2 years ago - 1 comment

#205 - samcomp

Issue - State: closed - Opened by rezarahman12 over 2 years ago

#204 - Where is the fold change value

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

#203 - eventalign_collapse error

Issue - State: closed - Opened by rezarahman12 over 2 years ago - 9 comments

#202 - About SK1 transcriptome reference and m6A sites for Yeast

Issue - State: open - Opened by Derryxu over 2 years ago - 1 comment

#201 - nanocompore sampcomp defunct

Issue - State: closed - Opened by zhongzhd over 2 years ago

#200 - 'event_l' referenced before assignment

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

#199 - SampComp error

Issue - State: open - Opened by rania-o almost 3 years ago - 5 comments

#198 - The problem in the output file

Issue - State: open - Opened by JeremyQuo almost 3 years ago - 1 comment

#197 - IndexError during Eventalign_collapse

Issue - State: closed - Opened by Tomcxf almost 3 years ago - 5 comments

#196 - The result database does not contain metadata

Issue - State: open - Opened by ynren1020 almost 3 years ago - 3 comments

#195 - Formatting issue on docs

Issue - State: open - Opened by mbhall88 almost 3 years ago

#194 - Code and data for Sup. Figure 10

Issue - State: closed - Opened by mbhall88 almost 3 years ago - 2 comments

#193 - SampCompDB plot position error

Issue - State: open - Opened by samir-watson over 3 years ago - 2 comments

#191 - swarmplot to visualize each replicate

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

#190 - Release v1.0.4

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

#189 - Improved logging/error handling in Whitelist

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

#188 - About nominal p-values

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

#187 - About GLMM p-value peaks passing 0.01

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

#186 - Is there CLI provision for transcript exclude list?

Issue - State: open - Opened by DrOllyGomez almost 4 years ago - 1 comment
Labels: enhancement

#185 - Dwell time scaling

Issue - State: open - Opened by tleonardi almost 4 years ago
Labels: enhancement

#184 - Ongoing transition to DB backend (SQLite)

Pull Request - State: open - Opened by hendrikweisser almost 4 years ago - 11 comments

#183 - DataStore: implement '__store_kmer'

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

#182 - Version 1.0.3 is shown as version 1.0.2

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

#180 - Release 1.0.3

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

#179 - Release 1.0.3

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

#178 - Fix error in deprecated CLI option

Pull Request - State: closed - Opened by a-slide about 4 years ago - 1 comment

#177 - SampComp output is a .dat file

Issue - State: closed - Opened by sr8510 about 4 years ago - 3 comments

#176 - Error with parsing bed file

Issue - State: closed - Opened by nemitheasura about 4 years ago - 7 comments

#175 - [ERROR - MainProcess | High fraction of invalid kmers]

Issue - State: closed - Opened by wososa about 4 years ago - 3 comments

#174 - [File Size and Run time] Nanocompore for 4 million reads

Issue - State: closed - Opened by wososa about 4 years ago - 12 comments

#173 - Documentation website not up to date

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

#171 - Release 1.0.2

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

#169 - Python 3.9 support

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

#167 - Nanopolishcomp merge

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

#166 - Modifications in DNA samples

Issue - State: closed - Opened by Stautis about 4 years ago - 6 comments

#165 - Feature disable anova

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

#164 - Invalid kmers filtering

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

#163 - Nanocompore gets stuck due to large amounts of data for a single transcript

Issue - State: open - Opened by tleonardi about 4 years ago
Labels: bug, Work in progress

#162 - Release 1.0.1

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

#161 - Poetry based versioning

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

#160 - Fixes for failing tests reported in #156

Pull Request - State: closed - Opened by tleonardi about 4 years ago - 1 comment

#159 - Dependencies bumped

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

#158 - No progress in the data processing step

Issue - State: closed - Opened by ploy-np about 4 years ago - 3 comments

#157 - Run SampComp error

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

#156 - test_TxComp.py:104: AssertionError

Issue - State: closed - Opened by deniskristak about 4 years ago - 5 comments
Labels: bug, Triage

#155 - The output file

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

#154 - nanocompore suspended

Issue - State: closed - Opened by lingolingolin over 4 years ago - 19 comments

#153 - NanocomporeError: Required fields not found in the data file

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

#151 - Analyze the nanocompore result

Issue - State: closed - Opened by aman21392 over 4 years ago - 1 comment

#150 - Do you have any software that can replace nanopolish？

Issue - State: closed - Opened by q1134269149 over 4 years ago - 1 comment

#149 - control samples of replicates

Issue - State: open - Opened by LeilyR over 4 years ago - 3 comments

#148 - Error when scaling for plotting

Issue - State: open - Opened by tleonardi over 4 years ago
Labels: bug

#146 - Speed up by filtering the comparison positions at SampComp step

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

#145 - Error occurred during SampCompDB command

Issue - State: closed - Opened by aman21392 over 4 years ago - 1 comment

#144 - importing error in pyhton API

Issue - State: closed - Opened by aman21392 over 4 years ago - 4 comments

#143 - Regarding SampCompDB issues

Issue - State: closed - Opened by aman21392 over 4 years ago - 2 comments

#142 - Installing problem of nanocompore

Issue - State: closed - Opened by aman21392 over 4 years ago - 2 comments

#141 - standard deviation in in silico datasets

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

#140 - Errors thrown by worker processes are not raised by the main process

Issue - State: closed - Opened by tleonardi over 4 years ago - 1 comment
Labels: bug

#139 - Fix issue 120

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

#138 - Bug in min_coverage filter

Issue - State: closed - Opened by tleonardi over 4 years ago

#137 - Hotfix 1.0.0rc3

Pull Request - State: closed - Opened by tleonardi almost 5 years ago

#136 - Typo in header of shift_stats file

Issue - State: closed - Opened by tleonardi almost 5 years ago

#135 - Updated python dependencies

Pull Request - State: closed - Opened by tleonardi almost 5 years ago

#134 - Docs hotfix

Pull Request - State: closed - Opened by tleonardi almost 5 years ago

#133 - Add reads slot in ref_pos_dict to track read ids

Pull Request - State: open - Opened by tleonardi almost 5 years ago - 3 comments

#132 - SampCompDB error with bed file

Issue - State: closed - Opened by samir-watson almost 5 years ago - 3 comments

#131 - Conda packages for Nanocompore and NanopolishComp

Issue - State: closed - Opened by mmiladi almost 5 years ago - 4 comments
Labels: enhancement

#130 - Question about the available test methods and the input argument

Issue - State: closed - Opened by mmiladi almost 5 years ago - 3 comments
Labels: question

#129 - What type of signal is plotted

Issue - State: closed - Opened by lingolingolin almost 5 years ago - 4 comments
Labels: question

#128 - compressing the eventalign tsv files

Issue - State: closed - Opened by mmiladi almost 5 years ago - 6 comments
Labels: enhancement

#127 - nanocompore keeps running forever

Issue - State: closed - Opened by lingolingolin almost 5 years ago - 3 comments
Labels: duplicate

#126 - Output file with list of selected transcripts

Issue - State: closed - Opened by a-slide almost 5 years ago - 1 comment
Labels: enhancement