LinkageIO/Camoco issues and pull requests

#102 - Bump flask from 1.0.3 to 2.3.2

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#101 - Installation

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

#100 - getting access to the co-expression network

Issue - State: open - Opened by xtLiu2017 over 3 years ago

#99 - module 'sqlalchemy.engine' has no attribute 'RowProxy'

Issue - State: open - Opened by gsun2unl over 3 years ago

#98 - nthreads cannot be larger than environment variable "NUMEXPR_MAX_THREADS"

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

#97 - Error: No such file or directory: 'pip'

Issue - State: closed - Opened by xtLiu2017 almost 4 years ago - 1 comment

#96 - Getting access to Camoco co-expression network in script

Issue - State: open - Opened by mdanb over 4 years ago

#95 - error associated with installing camoco using python 3.7.4 on mac

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

#94 - fix fstring on value error output

Pull Request - State: closed - Opened by rroutsong about 5 years ago - 2 comments

#93 - SNP2Gene mapping breakdown bug

Issue - State: open - Opened by schae234 over 5 years ago - 1 comment

#92 - Add degree distribution at varying z-score cutoffs to health command

Issue - State: open - Opened by schae234 over 5 years ago

#91 - Add network image to health command

Issue - State: open - Opened by schae234 over 5 years ago

#90 - ImportError: cannot import name Timestamp

Issue - State: closed - Opened by hriday535 over 5 years ago - 1 comment

#89 - Camoco Installation Issue

Issue - State: closed - Opened by yenon118 over 5 years ago - 5 comments

#88 - odo now breaks with the newest pandas due to tslib deprecation

Issue - State: closed - Opened by monprin over 5 years ago - 11 comments
Labels: bug

#87 - How to export normalized data and genes belonging which network

Issue - State: closed - Opened by shenweima almost 6 years ago - 11 comments

#86 - install ERROR

Issue - State: closed - Opened by congzhouczcz almost 6 years ago - 4 comments

#85 - A better documentation

Issue - State: closed - Opened by hufnagelbarbara almost 6 years ago - 3 comments

#84 - Make py.test know where the default files are

Issue - State: closed - Opened by schae234 about 6 years ago

#83 - Does feature count method affect network structure?

Issue - State: closed - Opened by schae234 over 6 years ago - 1 comment
Labels: question

#82 - SNP to gene mapping can sometimes mess up overlap when genes overlap.

Issue - State: open - Opened by schae234 over 6 years ago
Labels: bug, feature request

#81 - Global degree does not change when changing significant edge value

Issue - State: open - Opened by MeeshCompBio over 6 years ago - 2 comments
Labels: bug, Difficulty Level: Easy

#80 - Deploy on Cyverse

Issue - State: closed - Opened by schae234 over 6 years ago - 2 comments
Labels: feature request, Difficulty Level: Medium

#79 - Add syntax highlighting for GettingStarted.md

Pull Request - State: closed - Opened by RaoOfPhysics almost 7 years ago - 1 comment

#78 - Add syntax highlighting for GettingStarted.md

Pull Request - State: closed - Opened by RaoOfPhysics almost 7 years ago - 5 comments

#77 - Additional Roadmap Tasks

Issue - State: closed - Opened by schae234 almost 7 years ago - 2 comments
Labels: feature request, RoadMapping

#76 - correct tiny typo :)

Pull Request - State: closed - Opened by annakrystalli almost 7 years ago - 1 comment

#75 - GWAS.set_strongest causes ontology inconsitency

Issue - State: closed - Opened by monprin almost 7 years ago - 1 comment
Labels: bug

#74 - Database Lock Problem

Issue - State: closed - Opened by monprin almost 7 years ago - 1 comment
Labels: bug

#73 - Specified Networkx Version, Fixed Parallel Bug

Pull Request - State: closed - Opened by monprin almost 7 years ago - 4 comments

#72 - Integrate Coveralls.io

Pull Request - State: closed - Opened by fuzzmz almost 7 years ago - 5 comments

#71 - Installation working on MacOS

Pull Request - State: closed - Opened by seraco almost 7 years ago - 5 comments

#70 - Add a coveralls badge to readme

Issue - State: closed - Opened by schae234 almost 7 years ago - 4 comments
Labels: hacktoberfest, Difficulty Level: Easy

#69 - Allow full installation using conda

Issue - State: closed - Opened by schae234 almost 7 years ago - 16 comments
Labels: hacktoberfest, Difficulty Level: Easy

#68 - Get TravisCI working for OSX

Issue - State: closed - Opened by schae234 almost 7 years ago - 7 comments
Labels: installation, hacktoberfest, Difficulty Level: Easy

#67 - Migrate the install.sh script to work with setup.py

Issue - State: closed - Opened by schae234 almost 7 years ago - 5 comments
Labels: hacktoberfest, Difficulty Level: Medium

#66 - Gene name hyphens get filtered out when using cob.from_table()

Issue - State: open - Opened by MeeshCompBio almost 7 years ago - 3 comments

#65 - Installation Failed

Issue - State: closed - Opened by abbycabs about 7 years ago - 3 comments
Labels: bug, installation

#64 - Full documentation

Issue - State: closed - Opened by schae234 about 7 years ago
Labels: duplicate, enhancement

#63 - Project Roadmap

Issue - State: closed - Opened by schae234 about 7 years ago - 2 comments
Labels: enhancement, feature request, RoadMapping

#62 - Overlap Enhancement

Pull Request - State: closed - Opened by monprin over 7 years ago

#61 - Ontology enrichment overwrites itself

Issue - State: closed - Opened by schae234 over 7 years ago - 1 comment
Labels: bug

#60 - attrs for Term loci do not get stored when put into an Ontology

Issue - State: closed - Opened by schae234 over 7 years ago - 1 comment

#59 - Overlap.py fix and linear model quick fix in COB.py

Pull Request - State: closed - Opened by MeeshCompBio over 7 years ago - 4 comments

#58 - cli overlap command fails

Issue - State: closed - Opened by MeeshCompBio over 7 years ago

#57 - Allow option for presence absence variation

Pull Request - State: closed - Opened by MeeshCompBio over 7 years ago - 2 comments

#56 - Two-tail GO, linkage fix, locality fix

Pull Request - State: closed - Opened by MeeshCompBio over 7 years ago

#55 - Implement Neighborhood Algorithm

Issue - State: closed - Opened by schae234 over 7 years ago - 2 comments
Labels: feature request

#54 - Clustering the Expr matrix by leaves is broken

Issue - State: closed - Opened by schae234 over 7 years ago - 1 comment
Labels: bug

#53 - Your documentation is bad and you should feel bad.

Issue - State: closed - Opened by schae234 over 7 years ago - 1 comment
Labels: enhancement, feature request

#52 - Store parent SNP in Overlap analysis

Issue - State: open - Opened by schae234 over 7 years ago
Labels: bug

#51 - Moved coex table to Blaze

Pull Request - State: closed - Opened by monprin over 7 years ago - 1 comment

#50 - Moved coex table to Blaze

Pull Request - State: closed - Opened by monprin over 7 years ago

#49 - Implement a GWAS enrichement based on SNP to gene mapping

Issue - State: open - Opened by schae234 over 7 years ago
Labels: feature request

#48 - Replaced feather with bcolz (Fixed)

Pull Request - State: closed - Opened by monprin almost 8 years ago - 2 comments

#47 - Replaced feather with bcolz

Pull Request - State: closed - Opened by monprin almost 8 years ago

#46 - Allow getting multiple GOTerms at Once

Issue - State: open - Opened by monprin almost 8 years ago - 4 comments
Labels: enhancement

#45 - min_single_sample_expr Filter

Issue - State: closed - Opened by orionzhou almost 8 years ago - 3 comments

#44 - using the del_dataset command does not remove MCL clusters

Issue - State: closed - Opened by schae234 almost 8 years ago - 1 comment
Labels: bug

#43 - Update on feather?

Issue - State: closed - Opened by schae234 almost 8 years ago - 3 comments
Labels: question

#42 - Segmentation fault when building large networks

Issue - State: closed - Opened by MeeshCompBio about 8 years ago - 9 comments

#41 - One tail vs two tailed GO term

Pull Request - State: closed - Opened by MeeshCompBio about 8 years ago - 3 comments

#40 - Expand options for building GOnts

Issue - State: closed - Opened by schae234 about 8 years ago
Labels: feature request

#39 - Cluster accessions in COB plot

Issue - State: closed - Opened by schae234 about 8 years ago - 1 comment
Labels: feature request

#38 - Retrieve all ontology terms associated with loci

Issue - State: closed - Opened by monprin about 8 years ago - 2 comments
Labels: feature request

#37 - rowid doesn't get reset when RefGen gets rebuilt

Issue - State: closed - Opened by schae234 about 8 years ago - 1 comment

#36 - Bug fixed subnetwork, coex_expr_index, and neighbors

Pull Request - State: closed - Opened by monprin about 8 years ago

#35 - Fixed a couple bugs I found in subnetwork and neighbors

Pull Request - State: closed - Opened by monprin about 8 years ago

#34 - Brought mem requirement for most thing under 16GB, dropped HDF5 in favor of Feather

Pull Request - State: closed - Opened by monprin about 8 years ago

#33 - Fixed plot label issue

Pull Request - State: closed - Opened by MeeshCompBio over 8 years ago

#32 - Install script fix

Pull Request - State: closed - Opened by MeeshCompBio over 8 years ago

#31 - Num Intervening does not always produce result

Issue - State: open - Opened by monprin over 8 years ago - 3 comments
Labels: bug

#30 - new cli command for gene neighbors

Pull Request - State: closed - Opened by MeeshCompBio over 8 years ago

#29 - Implement a better MCL interface in python

Issue - State: closed - Opened by schae234 over 8 years ago - 1 comment
Labels: feature request, hacktoberfest, Difficulty Level: Hard

#28 - GWAS GO-Simulations non constant candidates

Issue - State: open - Opened by schae234 over 8 years ago
Labels: bug

#27 - gene neighbors

Pull Request - State: closed - Opened by MeeshCompBio over 8 years ago - 1 comment

#26 - creating COB from .csv

Issue - State: closed - Opened by MeeshCompBio over 8 years ago - 3 comments

#25 - cli camoco health error

Issue - State: closed - Opened by MeeshCompBio over 8 years ago - 29 comments
Labels: bug

#24 - Import Datasets Code

Issue - State: closed - Opened by schae234 almost 9 years ago - 1 comment
Labels: feature request

#23 - Changing filtering parameters when building COB

Issue - State: closed - Opened by MeeshCompBio almost 9 years ago - 5 comments

#22 - Micro Array Test COB

Issue - State: closed - Opened by schae234 about 9 years ago - 1 comment
Labels: feature request

#21 - Made GO ontology, sped up base ontology, added aliases to refgen, fixed bug with config.

Pull Request - State: closed - Opened by monprin about 9 years ago - 1 comment

#20 - Made GO ontology, sped up base ontology, added aliases to refgen.

Pull Request - State: closed - Opened by monprin about 9 years ago

#19 - Made GO ontology, sped up base ontology, added aliases to refgen.

Pull Request - State: closed - Opened by monprin about 9 years ago

#18 - To Rectify libqhull.so.5 Import Error

Issue - State: closed - Opened by schae234 about 9 years ago - 1 comment
Labels: installation

#17 - Running Git LFS in order to run tests

Issue - State: closed - Opened by schae234 about 9 years ago
Labels: enhancement, installation

#16 - To Rectify libicui18n.so.48 Import Error

Issue - State: closed - Opened by monprin about 9 years ago - 1 comment
Labels: installation

#15 - MCL requirement

Issue - State: closed - Opened by schae234 about 9 years ago - 5 comments
Labels: installation

#14 - Fixes to Onotology for base class purposes.

Pull Request - State: closed - Opened by monprin about 9 years ago - 1 comment

#13 - Stripped down ontology.

Pull Request - State: closed - Opened by monprin about 9 years ago - 1 comment

#12 - Added comparison class.

Pull Request - State: closed - Opened by monprin about 9 years ago - 1 comment

#11 - Added first draft of comparison class.

Pull Request - State: closed - Opened by monprin about 9 years ago - 2 comments

#10 - Comparing COBS with Gene Ontology (and others)

Issue - State: closed - Opened by schae234 about 9 years ago - 4 comments
Labels: feature request

#9 - Added compare_degree function and striping of quotes in gffs

Pull Request - State: closed - Opened by monprin about 9 years ago - 1 comment

#8 - Test Suite

Issue - State: closed - Opened by schae234 about 9 years ago - 1 comment
Labels: question

#6 - Networks from different count metrics

Issue - State: closed - Opened by schae234 about 9 years ago - 2 comments
Labels: enhancement

#5 - No default .camoco.conf file

Issue - State: closed - Opened by schae234 about 9 years ago - 1 comment
Labels: installation

#4 - Installation Experience

Issue - State: closed - Opened by monprin over 9 years ago
Labels: enhancement

#2 - Effective candidates

Issue - State: closed - Opened by schae234 over 9 years ago - 1 comment
Labels: bug

#1 - Static Layout

Issue - State: closed - Opened by schae234 over 9 years ago
Labels: enhancement

GitHub / LinkageIO/Camoco issues and pull requests