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
#1819 - Single fasta file containing all samples and requences into a usable format for dada2 analysis
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
#1809 - Aborted R session with DADA2 run for a large number of PacBio-sequenced samples
Issue -
State: open - Opened by emankhalaf about 1 year ago
- 11 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
#1795 - ITS filterAndTrim: No reads passed the filter + Denoising Errors dadaFs/Rs <- dada()
Issue -
State: open - Opened by jordan-dwm 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
#1788 - (DADA ITS) Error in filterAndTrim(cutFs, filtFs, cutRs, filtRs, maxN = 0, maxEE = c(2, :
Issue -
State: closed - Opened by Parikrama about 1 year ago
- 9 comments
#1787 - (ITS DADA2) Error in rval[sapply(rval, is.character)] : invalid subscript type 'list'
Issue -
State: open - Opened by Parikrama about 1 year ago
- 14 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
#1779 - 18S workflow in DADA2 issue:Error in h(simpleError(msg, call)) : Error evaluating 'x' parameter when selecting method for 'reverseComplement' function: key 70 (char 'F') not in lookup table
Issue -
State: open - Opened by hehanhhh about 1 year ago
- 5 comments
#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
#1776 - Question about merged read for assigning taxonomy by dada2 package in R
Issue -
State: open - Opened by chengcheng0625 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
#1771 - The number of ASVs is small, the data efficiency is low, and high-abundance sequences are filtered out.
Issue -
State: closed - Opened by zhangjl-work about 1 year ago
#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
#1763 - silva_nr99_v138.1_train_set.fa.gz is suitable for V3-V4 region taxonomic assignment?
Issue -
State: open - Opened by Tinh1425 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
#1755 - Error rates could not be estimated (this is usually because of very few reads)
Issue -
State: closed - Opened by ShailNair over 1 year ago
- 7 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
#1738 - Some input samples had no reads pass the filter --> Error rates could not be estimated (this is usually because of very few reads). Error in getErrors(err, enforce = TRUE) : Error matrix is NULL.
Issue -
State: open - Opened by chuynh96 over 1 year ago
- 14 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