Ecosyste.ms: Issues

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

GitHub / benjjneb/dada2 issues and pull requests

#1823 - FilterAndTrim for ITS sequences

Issue - State: open - Opened by hwangumn about 1 year ago - 3 comments

#1822 - Missing Taxonomy

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

#1821 - Availability of Greengenes2 database in DADA2 pipeline

Issue - State: closed - Opened by magibc about 1 year ago - 2 comments

#1820 - Issue with primer removal step

Issue - State: open - Opened by anamariamunizrodriguez about 1 year ago - 2 comments

#1818 - DADA2 stand alone output and LotuS2 - DADA2 produces different outcomes

Issue - State: open - Opened by Balaveer about 1 year ago - 2 comments

#1817 - assignTaxonomy function returned results that are mostly NA

Issue - State: open - Opened by Canxis about 1 year ago - 2 comments

#1816 - Cutadapt removal of primer

Issue - State: open - Opened by luisymbio about 1 year ago - 6 comments

#1815 - issue with qiime dada2 denoise-ccs

Issue - State: open - Opened by daisykuma22 about 1 year ago - 1 comment

#1814 - seqtab.rds to .fasta with sample names

Issue - State: closed - Opened by LukeLikesDirt about 1 year ago - 2 comments

#1813 - Filtering Phyla that have low feature prevalence

Issue - State: open - Opened by Ecotone23 about 1 year ago - 8 comments

#1812 - parallelization in filterAndTrim for Window OS

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

#1811 - Remove a cycle without discarding reads

Issue - State: open - Opened by ajaltomare about 1 year ago - 3 comments

#1810 - Parallelization with dada2 big data workflow

Issue - State: closed - Opened by luisymbio about 1 year ago - 4 comments

#1808 - How long does it take for R to assign fungal taxonomies?

Issue - State: open - Opened by LordoftheMelons about 1 year ago - 3 comments

#1807 - Removing primers with trimLeft

Issue - State: open - Opened by nuorenarra about 1 year ago - 2 comments

#1806 - The lengths are different between dereps an dadas

Issue - State: open - Opened by suzywang116 about 1 year ago - 10 comments

#1805 - Error in is(obj, "matrix") : object 'errF' not found

Issue - State: open - Opened by KOMALSKK about 1 year ago - 3 comments

#1804 - errf

Issue - State: open - Opened by KOMALSKK about 1 year ago

#1803 - denoise-ccs for ITS

Issue - State: open - Opened by Hobgoblin8 about 1 year ago - 1 comment

#1802 - Losing reads after removing chimera

Issue - State: closed - Opened by osidaksjdmw about 1 year ago - 2 comments

#1801 - ggplot2 issue

Issue - State: closed - Opened by nstrom1 about 1 year ago - 1 comment

#1800 - asigntaxonomy command and taxlevels argument

Issue - State: open - Opened by Guillermouceda about 1 year ago - 3 comments

#1799 - Problem after removing chimera steps

Issue - State: closed - Opened by sskoldas about 1 year ago - 4 comments

#1798 - PacBio 16S sequence-reg

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

#1797 - Filter plants contigs after dada2 ITS workflow

Issue - State: closed - Opened by laisoemis about 1 year ago - 1 comment

#1796 - Error with taxonomic assignment in 16s analysis

Issue - State: closed - Opened by Sada-mwatelah about 1 year ago - 2 comments

#1794 - errF <- learnErrors

Issue - State: closed - Opened by genesandbones about 1 year ago - 2 comments

#1793 - error loading quality score plots

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

#1792 - Error in removeBimeraDenovo

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

#1791 - Trimming Suggestion for 16S V3

Issue - State: closed - Opened by Jiayonglai123 about 1 year ago - 4 comments

#1790 - DADA2: Filtering and Trimming

Issue - State: open - Opened by Lightcrane-h about 1 year ago - 1 comment

#1789 - Combining ASV feature table and taxonomy table?

Issue - State: closed - Opened by skose82 about 1 year ago - 2 comments

#1786 - why do i have empty ASVs after running the dada function?

Issue - State: closed - Opened by gabrielet about 1 year ago - 2 comments

#1785 - % similarity against best match for each ASV

Issue - State: open - Opened by Paoluxxe about 1 year ago - 3 comments

#1784 - zero unclassified taxa at genus level?

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

#1783 - Making a custom LSU database with DADA2 from Silva files

Issue - State: open - Opened by JFranklin5221 about 1 year ago - 6 comments

#1782 - DADA2 makeTaxonomyFasta_SilvaNR

Issue - State: closed - Opened by JFranklin5221 about 1 year ago

#1781 - Missing samples in bar plot

Issue - State: open - Opened by arna3 about 1 year ago - 12 comments

#1780 - Error models and ASV detection

Issue - State: closed - Opened by zinfin about 1 year ago - 1 comment

#1778 - memory leak during learnErrors

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

#1777 - OTUs from V4 region of 16S rRNA assigned as eukaryota

Issue - State: open - Opened by Ecotone23 about 1 year ago - 4 comments

#1775 - Question about reverse complement in assignTaxonomy

Issue - State: open - Opened by mtsiknia about 1 year ago - 2 comments

#1774 - Dealing with Variable Sequence Lengths in DADA2

Issue - State: open - Opened by alexandriai168 about 1 year ago - 1 comment

#1773 - Too many ASVs in mock community

Issue - State: open - Opened by rachel-1212 about 1 year ago - 2 comments

#1772 - Loosing alot of reads

Issue - State: open - Opened by MadsBjornsen about 1 year ago - 5 comments

#1770 - Issue with taxa assignment using custom database

Issue - State: open - Opened by MGMarine about 1 year ago - 7 comments

#1769 - 16S V4 region frequently occurring sequences at start of R1 and R2

Issue - State: open - Opened by johannalheureux23 over 1 year ago - 6 comments

#1768 - Most of my ITS ASV's map to Other (>60%)

Issue - State: open - Opened by hereformore over 1 year ago - 6 comments

#1767 - ITS cutadapt primer trimming

Issue - State: closed - Opened by ImperialBV over 1 year ago - 6 comments

#1766 - mergePairs issues

Issue - State: open - Opened by kemerson3 over 1 year ago - 2 comments

#1765 - Merging sequence tables from different runs and different amplicons.

Issue - State: closed - Opened by Varun9599 over 1 year ago - 5 comments

#1764 - addSpecies database doesn't entirely match silva

Issue - State: closed - Opened by korneeld over 1 year ago - 2 comments

#1762 - AlignSeqs error

Issue - State: closed - Opened by tandrafraser over 1 year ago - 10 comments

#1761 - Cast integer objects to numeric type to handle large integers

Pull Request - State: open - Opened by ycl6 over 1 year ago

#1760 - dada2: Removal of singletons and non-bacterial ASVs

Issue - State: closed - Opened by kemerson3 over 1 year ago - 3 comments

#1759 - FilterAndTrim

Issue - State: closed - Opened by hadeerIsmail22 over 1 year ago - 2 comments

#1753 - Taxonomic assignment issue on mock community from Zymo

Issue - State: closed - Opened by chrissy005 over 1 year ago - 9 comments

#1751 - Meta-analysis-different primers

Issue - State: open - Opened by Balakulandai over 1 year ago - 9 comments

#1750 - DECIPHER: IdTaxa Run Time Question

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

#1748 - issue in quality profile plots caused by ggplot2 3.3.4

Issue - State: open - Opened by ep142 over 1 year ago - 3 comments

#1747 - "NAs produced by integer overflow" when running learnErrors

Issue - State: closed - Opened by ycl6 over 1 year ago - 3 comments

#1744 - Batch effects and small sample size

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

#1729 - DADA2 Trimming Parameter Automation

Issue - State: closed - Opened by alexandriai168 over 1 year ago - 1 comment

#1711 - problem with mergePairs

Issue - State: closed - Opened by cabraham03 over 1 year ago - 2 comments

#1680 - Updated GreenGenes database formatting for DADA2

Issue - State: open - Opened by cfrancoeur over 1 year ago - 22 comments
Labels: enhancement, Priority

#1674 - DNBseq takes forever to run

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

#1659 - Error with derepFastq

Issue - State: open - Opened by ChristinaOvergaard almost 2 years ago - 5 comments

#1656 - Filtering and trimming dada2

Issue - State: open - Opened by MathildeJqt almost 2 years ago - 3 comments

#1652 - Run DADA2 for multiple studies

Issue - State: open - Opened by ghost almost 2 years ago - 3 comments

#1645 - learnErrors, dada and removeBimeraDenovo result in ‘caught segfault’ error

Issue - State: open - Opened by petrijp almost 2 years ago - 14 comments

#1628 - creating a reference DB to assign taxonomy in Dada2

Issue - State: open - Opened by mycotonia3 almost 2 years ago - 11 comments

#1612 - unite database assignment of host sequences

Issue - State: open - Opened by connor-morozumi about 2 years ago - 12 comments
Labels: documentation

#1526 - Custom Taxonomy Training Set

Issue - State: closed - Opened by RFlazcano over 2 years ago - 6 comments

#1523 - Error in readBin(con, raw(), n) : error reading from the connection

Issue - State: open - Opened by ninglinwang over 2 years ago - 6 comments

#1520 - dada2 pipeline for metabarcoding

Issue - State: closed - Opened by safiqu over 2 years ago - 7 comments

#1456 - Issues with data frame making

Issue - State: open - Opened by AkilaMuthalagu almost 3 years ago - 6 comments

#1421 - Error in getUniques(x) when running sapply(dadaFs, getN)

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

#1404 - Problems with install DADA2 in R version 4.1

Issue - State: open - Opened by Alejandra31pucv about 3 years ago - 18 comments

#1376 - Non-zero exit status.

Issue - State: closed - Opened by edmundtayzy about 3 years ago - 1 comment

#1375 - Support for Apple M1 arch64

Issue - State: closed - Opened by akhst7 about 3 years ago - 8 comments

#1374 - Is it valid to calculate Good's coverage for DADA2 output ?

Issue - State: closed - Opened by ShailNair about 3 years ago - 2 comments

#1373 - Possible to show 'top 3' taxonomy assignments?

Issue - State: closed - Opened by eefj33 about 3 years ago - 1 comment

#1371 - converting multi-level taxonomy of OTUs to 7-level taxonomy

Issue - State: closed - Opened by alinawazfcc about 3 years ago - 1 comment

#1368 - Remove chimeras, consensus vs. pooled

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

#1367 - Error in filterAndTrim

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

#1364 - Nanopore variable region sequencing analysis

Issue - State: open - Opened by CarlaCristinaUranga over 3 years ago - 8 comments
Labels: question

#1363 - Abundance of dereplicated and denoised reads doesn't match

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

#1362 - Error Message

Issue - State: closed - Opened by markdjohnson over 3 years ago - 5 comments

#1361 - Reproducing DADA2 output of the Extreme data set

Issue - State: closed - Opened by NicolasNaepflin over 3 years ago - 1 comment