qiyunzhu/woltka issues and pull requests

#215 - Upgrading Python packaging mechanism

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#214 - updated dependency

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#213 - Merge pull request #212 from qiyunzhu/0.1.7

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#212 - upgrading to 0.1.7

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#211 - Sequence depth normalization after woltka classification

Issue - State: open - Opened by UniAlberta about 2 months ago - 4 comments

#210 - Improved vectorized ordinal mapper

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#209 - Formalized the NumPy + Numba solution for ordinal mapper

Pull Request - State: closed - Opened by qiyunzhu about 2 months ago

#208 - missing column labels when running woltka classify on individual samfile

Issue - State: closed - Opened by sherlyn99 6 months ago - 2 comments

#207 - [Bug] KEGG database is missing reactions in certain modules

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

#206 - Provide organism agnostic version of pathway_mbrs.txt in the backend via EC numbers

Issue - State: open - Opened by jolespin 7 months ago

#205 - Improved handling of range coordinates

Pull Request - State: closed - Opened by qiyunzhu 7 months ago

#204 - Coverage stop coordinate switch to exclusive

Pull Request - State: closed - Opened by wasade 7 months ago - 4 comments

#203 - Trying to build a phylogenetic tree using output in Qiita

Issue - State: open - Opened by lrt666 8 months ago

#202 - Change back changelog links

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#201 - Replaced links in changelog

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#200 - AssertionError: Conflicting values found for "RXN-13667".

Issue - State: open - Opened by deppworld 9 months ago - 8 comments

#199 - Upgrading to v0.1.6

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#198 - Restoring commits

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#197 - Updated documentation

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#196 - updated coveralls version

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#195 - fixing coverage

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#194 - fixing github actions

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#193 - fixing github actions

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#192 - Added exclusion set, and multiple optimizations

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#191 - Improved paired-end SAM processing

Pull Request - State: closed - Opened by qiyunzhu 9 months ago

#190 - Added q2 unit tests

Pull Request - State: closed - Opened by qiyunzhu 10 months ago

#189 - added streamline docs

Pull Request - State: closed - Opened by qiyunzhu 11 months ago

#188 - match reads with genes:gloc = genes_pop(code & (1 << 30) - 1) KeyError: 3603

Issue - State: open - Opened by Dexter5577 about 1 year ago - 10 comments

#187 - KEGG pathways detected are not represented in pathway coverage results

Issue - State: open - Opened by LLansing over 1 year ago - 1 comment

#186 - AssertionError: Conflicting values found for "1111886".

Issue - State: open - Opened by liushuqing506 over 1 year ago - 3 comments

#185 - How to get the phylogenetic tree after following the recommended process to get table.biom

Issue - State: open - Opened by diego00012138 over 1 year ago - 1 comment

#184 - ValueError: cannot call `vectorize` on size 0 inputs unless `otypes` is set

Issue - State: open - Opened by samd1993 over 1 year ago

#183 - BUG: Ignore hidden files when reading directory

Pull Request - State: closed - Opened by ElDeveloper over 1 year ago

#182 - Added PAF format support

Pull Request - State: closed - Opened by qiyunzhu over 1 year ago

#181 - futher updated change log

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#180 - updated change log

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#179 - For version 0.1.5

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#178 - Upgrading to version 0.1.5

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#177 - Backward compatibility

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#176 - Improve command-line interface

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#175 - tweaked biom rounding

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#174 - updated install doc

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#173 - added suffix collapse

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago - 1 comment

#172 - fixed coverage issue

Pull Request - State: closed - Opened by qiyunzhu almost 2 years ago

#171 - BUG/PERF: avoid dense conversion of biom

Pull Request - State: closed - Opened by wasade almost 2 years ago - 2 comments

#170 - [SUGGESTED FEATURE] Dockerized Woltka with numba acceleration

Issue - State: open - Opened by Dane-Z almost 2 years ago

#169 - DOC: Add note about MetaCyc classify/collapse

Pull Request - State: closed - Opened by ElDeveloper about 2 years ago - 3 comments

#168 - Data Transformations after Functional classification of genes

Issue - State: closed - Opened by jlabus over 2 years ago - 1 comment

#167 - different results between classify directly and collapse after

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

#166 - Finding strains and sub-species on WoL

Issue - State: closed - Opened by JenniferOnuora over 2 years ago - 1 comment