SegataLab/panphlan issues and pull requests

#42 - Duplicated sequences in reference fasta

Issue - State: open - Opened by robbueck 2 months ago

#41 - I must merge the Pair-ends metagenomic data together, and then starting running the panphlan mapping.

Issue - State: open - Opened by allen-zhan340 about 1 year ago

#40 - Problem with download reference genome from PanPhlAn pangenome database

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

#39 - panphlan_clean_pangenome.py isn't installed as part of the package

Issue - State: open - Opened by sterrettJD almost 2 years ago

#38 - How to import roary pangenome results into panphlan?

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

#37 - Index for manual {species}_pangenome.tsv

Issue - State: open - Opened by Hocnonsense over 2 years ago

#36 - missing link `How to find and download reference genomes from NCBI?`

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

#35 - Error running the sample a second time

Issue - State: open - Opened by namdeka about 3 years ago - 1 comment

#34 - Duplicate sequence in Cardiobacterium hominis pangenome

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

#33 - <mpileup> Set max per-file depth to 8000: What is it?

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

#32 - panphlan_map.py (ERR): bowtie2-align exited with value 134 'std::bad_alloc'

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

#31 - Prevent Panphlan from rejecting all mapped reads when the --th_mismat…

Pull Request - State: closed - Opened by fplaza over 3 years ago - 2 comments

#30 - reference pangenome not available

Issue - State: closed - Opened by xzl0034 almost 4 years ago - 2 comments

#29 - Using RAST annotations

Issue - State: closed - Opened by minna-miha almost 4 years ago - 2 comments

#28 - Lactobacillus case and Lactobacillus paracasei

Issue - State: closed - Opened by qinglong89 almost 4 years ago - 1 comment

#27 - --func_annot

Issue - State: open - Opened by nick-youngblut almost 4 years ago - 6 comments

#26 - speed up panphlan_map.py with intervaltree?

Issue - State: open - Opened by nick-youngblut about 4 years ago

#25 - panphlan_download_pangenome.py: panphlan_pangenomes_links.tsv written to cwd

Issue - State: closed - Opened by nick-youngblut about 4 years ago

#24 - panphlan_profiling.py: allow user to specify input files

Issue - State: closed - Opened by nick-youngblut about 4 years ago

#23 - panphlan bioconda recipe is incomplete

Issue - State: closed - Opened by nick-youngblut about 4 years ago - 1 comment

#22 - panphlan_map.py: Cannot set temporary directory location

Issue - State: closed - Opened by nick-youngblut about 4 years ago - 5 comments

#21 - panphlan_download_pangenome.py: number of retries

Issue - State: closed - Opened by nick-youngblut about 4 years ago - 10 comments

#20 - Error running panphlan_map

Issue - State: open - Opened by sanpande about 4 years ago - 6 comments

#19 - Meet “OSError: Invalid data stream” when using panphlan_profiling.py

Issue - State: closed - Opened by siriusorignblack about 4 years ago - 11 comments

#18 - working with mapping files - enquiries

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

#17 - Duplicated sam header error in panphlan_map.py

Issue - State: closed - Opened by AUAShen over 4 years ago - 5 comments

#16 - IndexError: list index out of range

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

#15 - UniRef90 genes to function

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

#14 - pangenomes corrupted

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

#13 - problems with using standard input

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

#12 - Track unknown strains

Issue - State: closed - Opened by termithorbor over 4 years ago - 5 comments

#11 - Wiki installation

Issue - State: closed - Opened by fbeghini over 4 years ago
Labels: documentation

#10 - Paired end reads

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

#9 - Added setup.py installer for PyPi package

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

#8 - PanPhlAn RNA-seq using latest version of panphlan

Issue - State: closed - Opened by fconstancias over 4 years ago - 7 comments

#7 - HUMAnN2_CHOCOPhlAn_201901_functional_annotation_mapping.tsv

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

#6 - about the filename extension

Issue - State: closed - Opened by dytk2134 over 4 years ago - 4 comments

#5 - NameError: name 'randint' is not defined during panphlan_profiling.py

Issue - State: open - Opened by fconstancias over 4 years ago - 7 comments

#4 - Where to download pangenome file of a species?

Issue - State: closed - Opened by lz870718 over 4 years ago - 6 comments

#3 - NotADirectoryError: [Errno 20] Not a directory: False

Issue - State: closed - Opened by zckoo007 almost 5 years ago - 1 comment

#2 - How to obtain chocophlan pangenome.csv?

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

#1 - Dev leo

Pull Request - State: closed - Opened by leonarDubois almost 5 years ago - 1 comment

GitHub / SegataLab/panphlan issues and pull requests