Ecosyste.ms: Issues

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

GitHub / biocore/qiime issues and pull requests

#2234 - update qiime.org landing page

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

#2233 - Multiple_join_paired_ends.py output files names

Issue - State: open - Opened by chwang740 about 2 years ago

#2231 - Problems using count_seqs.py with joined reads

Issue - State: open - Opened by andso17 almost 3 years ago - 1 comment

#2230 - I got problem when running qiime2 env

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

#2229 - I have a big problem help me!!

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

#2227 - Help with ClustalW..

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

#2226 - Basespace Google key issue

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

#2224 - Heatmap does not show differentiation

Issue - State: open - Opened by nicey1995 over 5 years ago

#2223 - OTU table including fasta sequences

Issue - State: open - Opened by arsilan324 over 5 years ago

#2222 - Alpha Diversity Boxplots

Issue - State: open - Opened by Newman-Wang over 5 years ago

#2221 - Symbols

Issue - State: open - Opened by ma680 almost 6 years ago

#2220 - unable to install usearch

Issue - State: open - Opened by jdhenaos about 6 years ago

#2219 - info -e

Issue - State: open - Opened by megthommes about 6 years ago

#2218 - Why some of the samples are missing during OTU picking?

Issue - State: closed - Opened by arsilan324 about 6 years ago - 1 comment

#2217 - Alpha_rarefraction.py error

Issue - State: open - Opened by santhoshnh about 6 years ago - 1 comment

#2215 - incorrect value for phred_offset in qiime

Issue - State: open - Opened by hallerliran over 6 years ago - 1 comment

#2144 - DOC: updates to point new devs toward QIIME 2

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

#2136 - error of rdp classifier by using assign_taxonomy.py in qiime

Issue - State: closed - Opened by KaiFeng007 over 8 years ago - 6 comments

#2105 - link Bokulich et al mock community test files from the QIIME Resources page

Issue - State: open - Opened by gregcaporaso about 9 years ago - 34 comments
Labels: quick fix, website

#2083 - Provide the possibility to split demultiplexed files by sample, allow…

Pull Request - State: closed - Opened by zachcp about 9 years ago - 11 comments

#2082 - Feature Request: splitting demultiplexed fastq.

Issue - State: closed - Opened by zachcp about 9 years ago - 2 comments

#2058 - error on assign_taxonomy.py

Issue - State: open - Opened by wentyqq over 9 years ago - 2 comments

#2037 - identify_paired_differences usability enhancement

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 6 comments

#2032 - updates for 1.9.1-dev

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 3 comments

#2031 - 1.9.1 release

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 2 comments

#2029 - jackknifed beta diversity updates

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 2 comments

#2027 - observation_metadata_correlation.py bug fix

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 1 comment

#2021 - added ability to pass runtime limit to start_parallel_jobs_slurm.py

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 4 comments

#1998 - several quick fixes

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 4 comments

#1990 - remove BLAST DB formatting from parallel pynast wrapper

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 2 comments

#1986 - update minimum biom version in QIIME for testing

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 4 comments

#1969 - KeyError

Issue - State: closed - Opened by bwawrik over 9 years ago - 3 comments

#1963 - filter_taxa_from_otu_table.py uninformative error

Issue - State: closed - Opened by wdwvt1 over 9 years ago - 13 comments
Labels: bug, waiting-for-merge

#1958 - adds convergent mode to pick_open_reference_otus

Pull Request - State: closed - Opened by gregcaporaso over 9 years ago - 5 comments

#1920 - fixing issues and updating version strings for 1.9.0

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#1910 - changed default confidence threshold for Naive Bayes classifiers

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 4 comments

#1907 - documentation updates

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#1880 - performance improvement for split_libraries_fastq.py

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 3 comments

#1877 - updated notebooks for 1.9.0

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago

#1846 - QIIME 1.9.0-rc2

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#1845 - QIIME 1.9.0-rc2

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 7 comments

#1815 - QIIME 1.9.0 release candidate 1

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 2 comments

#1814 - addition of differential_abundance.py and normalize_table.py

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 2 comments

#1808 - updates to script index and associated documentation

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 1 comment

#1803 - some fixes to compute_taxonomy_ratio.py to get tests passing and clarify docs

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 2 comments

#1800 - removes summarize_otu_by_cat.py in favor of collapse_samples.py

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 2 comments

#1791 - removed make_otu_heatmap_html.py

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 6 comments

#1761 - updates to print_qiime_config.py

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 3 comments

#1751 - small improvements to help text, fixes #1750

Pull Request - State: closed - Opened by gregcaporaso almost 10 years ago - 3 comments

#1712 - added output of raw data for paired difference testing

Pull Request - State: closed - Opened by gregcaporaso about 10 years ago - 6 comments

#1711 - TST/REVERT: reduction of the runtime of the test

Pull Request - State: closed - Opened by gregcaporaso about 10 years ago - 1 comment

#1700 - update for skbio 0.2.1

Pull Request - State: closed - Opened by gregcaporaso about 10 years ago - 8 comments

#1693 - add script for collapsing replicate samples

Pull Request - State: closed - Opened by gregcaporaso about 10 years ago - 10 comments
Labels: enhancement

#1685 - adds new function to support #1678

Pull Request - State: closed - Opened by gregcaporaso about 10 years ago - 8 comments

#1639 - MAINT: updated numpy dependency to 1.7.1 or later, fixes #1494

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 3 comments

#1570 - fixed broken link

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 1 comment

#1560 - fixes build error that resulted from denoiser changes

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 1 comment

#1539 - work on removing cogent dependency and handling an skbio interface change

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 4 comments

#1503 - removes dependence on cogent's Sequence object

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 3 comments

#1420 - Remove protein

Pull Request - State: closed - Opened by gregcaporaso over 10 years ago - 1 comment

#1401 - fixes issue 1400

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 5 comments

#1386 - fixes issue 258

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 4 comments

#1289 - fixed error in formatting of help string

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 1 comment

#1280 - added more informative error message for common issue

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 2 comments

#1279 - addition of developer documentation

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 4 comments

#1271 - all otu pickers now perform some validation on input file

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 4 comments

#1270 - updated qiime.parse.parse_taxonomy to strip whitespace from taxa strings

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 3 comments

#1250 - updated so script usage test output from all_tests.py is more informative

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 2 comments

#1249 - fixes bug in core_diversity_analyses.py

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 7 comments

#1245 - fixed error in documentation; partially addresses #531

Pull Request - State: closed - Opened by gregcaporaso almost 11 years ago - 6 comments

#1225 - Bug: Formatdb is deprecated.

Issue - State: closed - Opened by zachcp about 11 years ago - 2 comments

#1202 - updated to make uclust the default taxonomic assignment method

Pull Request - State: closed - Opened by gregcaporaso about 11 years ago - 15 comments

#1159 - changed default similarity to 0.90

Pull Request - State: closed - Opened by gregcaporaso about 11 years ago - 2 comments

#1103 - Add absolute minimum read length option to split_libraries_fastq.py

Issue - State: closed - Opened by nr0cinu about 11 years ago - 3 comments

#1021 - split_libraries_fastq.py can now handle per-sample, non-barcoded fastq files

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 6 comments

#1020 - updated transform_coordinate_matrices to take more than two input matrices

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 14 comments

#973 - Core failure recovery

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 5 comments

#967 - fixed issue where %prog was not replaced with script name

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago

#931 - tutorial updates

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 1 comment

#880 - some edits on top of @johnchase's SourceTracker tutorial

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 5 comments

#877 - Doc edits

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 1 comment

#832 - updated to address #831

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 1 comment

#790 - QiimeCommand class prototype

Pull Request - State: closed - Opened by gregcaporaso over 11 years ago - 5 comments

#585 - updated handling of nan to address test failure

Pull Request - State: closed - Opened by gregcaporaso almost 12 years ago

#213 - rename _input_splitter to something more appropriate

Issue - State: open - Opened by gregcaporaso about 12 years ago - 1 comment
Labels: enhancement

#211 - centralize the functionality for building a blast database before starting a parallel run

Issue - State: open - Opened by gregcaporaso about 12 years ago - 1 comment
Labels: enhancement

#199 - persistent/transient community member code from QiimeUtils to QIIME

Issue - State: open - Opened by gregcaporaso about 12 years ago - 1 comment
Labels: enhancement

#194 - uclust pre-sort by abundance should collapse sequences which are prefixes of other sequences

Issue - State: open - Opened by gregcaporaso about 12 years ago - 4 comments
Labels: enhancement

#113 - workflow scripts should compress large but infrequently used directories

Issue - State: open - Opened by gregcaporaso about 12 years ago - 2 comments
Labels: enhancement

#108 - Missing dependencies send an error vs. a warning

Issue - State: open - Opened by gregcaporaso about 12 years ago - 1 comment
Labels: enhancement

#100 - core_qiime_analyses should only run distance histograms when categories is provided

Issue - State: closed - Opened by gregcaporaso about 12 years ago - 1 comment
Labels: enhancement

#99 - beta_diversity_through_plots.py parallel stalls when tree not provided

Issue - State: closed - Opened by gregcaporaso about 12 years ago - 2 comments
Labels: bug