Ecosyste.ms: Issues

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

GitHub / biocore/songbird issues and pull requests

#169 - songbird multinomial error: negative dimensions are not allowed

Issue - State: open - Opened by sherlyn99 over 1 year ago - 4 comments

#168 - Error running the standalone version of songbird

Issue - State: closed - Opened by pyjm over 1 year ago - 14 comments

#167 - q2-songbird biplot metadata issue

Issue - State: closed - Opened by pablocatarecha over 1 year ago - 4 comments

#166 - Qiime Songbird Multinomial - 'Data Frame' Error

Issue - State: closed - Opened by nagr4657 over 1 year ago - 14 comments

#165 - Is low values of Q2 fine to keep move forward for manuscript ?

Issue - State: closed - Opened by princy149 about 2 years ago - 2 comments

#164 - collapsing at taxa level and then use in songbird pipeline is right way or not?

Issue - State: closed - Opened by princy149 over 2 years ago - 2 comments

#162 - songbird installation with qiime2-2020.2 problem

Issue - State: closed - Opened by princy149 over 2 years ago - 4 comments

#160 - M1 12.2.1 Mackbook air problems with instalation of songbird

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

#159 - X axis of the CV error plots or tensorboard plots

Issue - State: open - Opened by manjumoorthy95 over 2 years ago - 4 comments

#158 - Problems with installation

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

#157 - Songbird Input format

Issue - State: closed - Opened by y3zhu over 2 years ago - 2 comments

#156 - REQUEST: any plan to package this for R?

Issue - State: closed - Opened by StfnRomano about 3 years ago - 1 comment
Labels: wontfix

#155 - Can songbird be used in a Jupyter notebook without command line wrappers?

Issue - State: open - Opened by jolespin about 3 years ago - 11 comments
Labels: question

#154 - README installation instructions don't seem to work

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

#153 - missing column in songbird output

Issue - State: open - Opened by bck243 over 3 years ago

#152 - Songbird tensorflow error

Issue - State: closed - Opened by JGADuBose over 3 years ago - 6 comments

#151 - songbird multinomial treating variables as categorical when they are numeric

Issue - State: closed - Opened by bck243 over 3 years ago - 7 comments

#150 - Plugin error from songbird: 'Testing'

Issue - State: closed - Opened by bck243 over 3 years ago - 4 comments

#148 - songbird 2?

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

#147 - Plugin error from songbird

Issue - State: closed - Opened by brunobohn7 almost 4 years ago - 7 comments

#145 - About filtering the input biom file

Issue - State: open - Opened by coralzhang almost 4 years ago - 5 comments

#144 - qiime2-2020.8 and songbird-1.0.3 unsatisfiable

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

#143 - Songbird usage approach

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

#142 - using a subset of samples

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

#141 - Memory errors for large datasets

Issue - State: open - Opened by mortonjt almost 4 years ago - 4 comments

#140 - Fix, test, and document filtering bug

Pull Request - State: closed - Opened by fedarko almost 4 years ago - 1 comment

#139 - Off-by-one errors in filtering?

Issue - State: closed - Opened by fedarko almost 4 years ago
Labels: bug

#138 - patsy.PatsyError: Error evaluating factor: NameError: name 'X' is not defined

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

#137 - ValueError: negative dimensions are not allowed

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

#136 - formatting full factorial formula

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

#135 - Multinomial regression continuous variable scaling

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

#134 - Using songbird standalone

Issue - State: open - Opened by coralzhang about 4 years ago - 5 comments

#133 - Error running songbird standalone

Issue - State: open - Opened by swokybio about 4 years ago - 7 comments

#132 - IndexError: Issue importing data into songbird?

Issue - State: closed - Opened by bck243 over 4 years ago - 2 comments

#131 - Statistical assumptions?

Issue - State: closed - Opened by shenjean over 4 years ago - 2 comments
Labels: question

#130 - log(a/b) - a and b values

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

#129 - confusing ID column names

Issue - State: open - Opened by KujawinskiLaboratory over 4 years ago - 1 comment

#128 - TypeError: SparseDataFrame() takes no arguments

Issue - State: open - Opened by sformel over 4 years ago - 6 comments
Labels: dependencies

#127 - Replace conda-forge with pip in Q2 install instructions

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

#126 - More QIIME 2 / TensorFlow conda-forge installation problems ._.

Issue - State: open - Opened by fedarko over 4 years ago - 6 comments
Labels: dependencies

#125 - Post release update

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#124 - Version 1.0.3

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#123 - REL: Relax minimum TF version to 1.15 from 1.15.2

Pull Request - State: closed - Opened by fedarko over 4 years ago

#122 - problem installing songbird 1.0.2 with qiime2-2020.2

Issue - State: closed - Opened by gwarmstrong over 4 years ago - 6 comments
Labels: dependencies

#121 - Stratified splitting to train/test in split_training

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

#120 - ModuleNotFoundError: No module named 'tensorflow.contrib'

Issue - State: closed - Opened by ghost over 4 years ago - 4 comments
Labels: question, dependencies

#119 - Interpretation of differentials

Issue - State: open - Opened by dadahan over 4 years ago - 7 comments
Labels: question

#118 - (Temporarily) pin pandas version in the README's standalone install instructions

Pull Request - State: closed - Opened by fedarko over 4 years ago - 2 comments

#117 - Pandas versions should be pinned to be below v1

Issue - State: open - Opened by fedarko over 4 years ago - 3 comments
Labels: dependencies

#116 - DOC: add another resource link to README

Pull Request - State: closed - Opened by fedarko over 4 years ago

#115 - Updating version

Pull Request - State: closed - Opened by mortonjt over 4 years ago

#114 - REL: fix typo re: TF vsn + elaborate in changelog

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

#113 - Getting Q-squared values for standalone Songbird?

Issue - State: open - Opened by fedarko over 4 years ago - 3 comments
Labels: enhancement, ui

#112 - Examples and/or more precise information on "good enough" data re: model fitting

Issue - State: open - Opened by fedarko over 4 years ago - 2 comments
Labels: docs

#111 - More exact tests

Issue - State: open - Opened by fedarko over 4 years ago
Labels: code internals

#110 - Upgrading to TensorFlow v2 or PyTorch

Issue - State: open - Opened by fedarko over 4 years ago - 2 comments
Labels: code internals, dependencies, future ideas

#109 - Add to README; bump / pin TF versions; other minor fixes

Pull Request - State: closed - Opened by fedarko over 4 years ago - 3 comments

#108 - ENH: Q2 summary interval allow float

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

#107 - Travis tests failing all of a sudden

Issue - State: closed - Opened by gibsramen over 4 years ago - 6 comments
Labels: code internals, dependencies

#106 - Suppression of warnings and (optionally) output

Pull Request - State: closed - Opened by gibsramen over 4 years ago - 2 comments

#105 - Suppress all output while running multinomial

Issue - State: closed - Opened by gibsramen over 4 years ago - 3 comments
Labels: ui

#103 - update README

Pull Request - State: closed - Opened by lisa55asil over 4 years ago - 1 comment

#102 - Make error message on invalid training column values more clear

Issue - State: open - Opened by fedarko over 4 years ago - 1 comment
Labels: ui

#101 - ENH: Set random seeds

Pull Request - State: closed - Opened by gwarmstrong almost 5 years ago - 10 comments

#100 - songbird issue apparently involving FeatureTable [Frequency] column lengths

Issue - State: closed - Opened by TizianaS92 almost 5 years ago - 2 comments

#99 - Issue 55

Pull Request - State: closed - Opened by mortonjt almost 5 years ago - 3 comments

#98 - Behavior of "minimum feature count" is incorrectly documented

Issue - State: closed - Opened by fedarko almost 5 years ago - 2 comments

#97 - Accounting for phylogenetic relation between samples in the formula?

Issue - State: open - Opened by Jigyasa3 almost 5 years ago - 1 comment
Labels: enhancement, wontfix, ui, future ideas

#96 - Installing standalone version of Songbird using pip

Issue - State: closed - Opened by Jigyasa3 almost 5 years ago - 2 comments

#95 - NEW: Add tensorboard hparams to CLI

Pull Request - State: closed - Opened by gwarmstrong almost 5 years ago - 4 comments

#94 - Repeated lines in MultRegression __init__

Issue - State: closed - Opened by gwarmstrong almost 5 years ago
Labels: code internals

#93 - Hyperparameter tunining with hparams in tensorboard

Issue - State: closed - Opened by gwarmstrong almost 5 years ago - 1 comment

#91 - Adding --p-logging-dir option

Issue - State: open - Opened by mortonjt almost 5 years ago - 1 comment
Labels: enhancement

#84 - add examples of how model fitting plots *should not* look?

Issue - State: open - Opened by fedarko almost 5 years ago - 2 comments
Labels: docs

#83 - Add explanations for what exactly "Intercept" differentials mean

Issue - State: open - Opened by fedarko almost 5 years ago - 4 comments
Labels: docs

#82 - Have better explanation for Q-squared values

Issue - State: open - Opened by mortonjt about 5 years ago
Labels: ui, docs

#81 - More Patsy formula examples in README? / More documentation on design matrices, ANOVA, etc.

Issue - State: open - Opened by fedarko about 5 years ago - 3 comments
Labels: docs

#78 - Detect and ignore #q2:types rows in standalone metadata input

Issue - State: open - Opened by fedarko about 5 years ago - 1 comment
Labels: bug

#75 - Accounting for different summary intervals in summarize-paired?

Issue - State: open - Opened by fedarko about 5 years ago - 4 comments
Labels: bug, wontfix

#71 - enabling logging again

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

#70 - Tensorboard and qiime2

Issue - State: open - Opened by mortonjt about 5 years ago - 10 comments
Labels: question, dependencies

#59 - pypi install

Issue - State: open - Opened by mortonjt about 5 years ago
Labels: dependencies

#58 - Installation of songbird within the 2019.4 qiime2 environment errors out

Issue - State: closed - Opened by CarrieBrown about 5 years ago - 6 comments

#54 - q2-Songbird: plotting regression-biplots issue

Issue - State: open - Opened by jaybake5 over 5 years ago - 5 comments
Labels: bug, question

#47 - Tenserflow issue with OpenMP

Issue - State: open - Opened by michoug over 5 years ago - 1 comment
Labels: bug, dependencies

#45 - Trim dependencies (and make consistent)

Issue - State: open - Opened by mortonjt over 5 years ago - 1 comment
Labels: dependencies

#42 - Fine tune summary legends

Issue - State: open - Opened by mortonjt over 5 years ago
Labels: enhancement, good first issue, ui

#35 - Null distribution?

Issue - State: open - Opened by mortonjt over 5 years ago
Labels: enhancement

#31 - numerical issues

Issue - State: open - Opened by mortonjt over 5 years ago - 1 comment
Labels: bug, good first issue

#29 - include colinearity discussion?

Issue - State: open - Opened by lisa55asil over 5 years ago - 1 comment
Labels: docs

#26 - install instructions

Issue - State: open - Opened by mortonjt over 5 years ago
Labels: docs, dependencies

#18 - biplot command for stand alone CLI

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

#13 - Switch to pytest

Issue - State: open - Opened by mortonjt about 6 years ago
Labels: dependencies

#7 - k-way poisson

Issue - State: open - Opened by mortonjt about 6 years ago
Labels: enhancement