Ecosyste.ms: Issues

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

GitHub / MrOlm/inStrain issues and pull requests

#206 - Quick question to make sure I understood the documentation

Issue - State: closed - Opened by jehaab 21 days ago - 2 comments

#205 - Input files

Issue - State: open - Opened by Pan1455 25 days ago - 1 comment

#204 - position in gene

Issue - State: open - Opened by gabrieleghiotto about 1 month ago - 1 comment

#202 - Whether sambamba influence the results

Issue - State: closed - Opened by 473021677 about 2 months ago - 2 comments

#201 - Can inStrain be used for profiling metagenomes containing eukaryotic populations

Issue - State: closed - Opened by DOieGYuan about 2 months ago - 1 comment

#198 - StbError and Could not cluster genomes

Issue - State: open - Opened by Swt623 2 months ago - 3 comments

#197 - Local variable 'stb' referenced before assignment

Issue - State: closed - Opened by asierFernandezP 4 months ago - 1 comment

#196 - error "No paired reads detected"

Issue - State: closed - Opened by mlcoleman 4 months ago - 1 comment

#196 - error "No paired reads detected"

Issue - State: closed - Opened by mlcoleman 4 months ago - 1 comment

#195 - Discrepancy in gene ID mapping on same positions in different samples

Issue - State: open - Opened by Sidduppal 4 months ago - 8 comments
Labels: bug

#194 - ask for help

Issue - State: closed - Opened by zbyloveyj 4 months ago - 1 comment

#193 - Question about inStrain compare SNV pooling for low coverage variants

Issue - State: closed - Opened by priscalim00 4 months ago - 1 comment

#192 - Clustering Error, StbError, and Memory Usage for inStrain Compare

Issue - State: closed - Opened by gillianpatton 4 months ago - 1 comment

#190 - Error for using conda install

Issue - State: closed - Opened by Xinpeng021001 6 months ago - 1 comment

#189 - Question about dRep for getting representative genome database?

Issue - State: closed - Opened by akques 7 months ago - 3 comments

#188 - pNpS_variants value

Issue - State: closed - Opened by ucassee 8 months ago - 4 comments

#187 - instrain compare --bams for pooled_SNV

Issue - State: closed - Opened by Lyylsys 8 months ago - 5 comments

#186 - command "instrain profile " export that some plots can't make

Issue - State: closed - Opened by Quzelei 9 months ago - 3 comments

#185 - Detailed calculation of breadth (and coverage)

Issue - State: closed - Opened by anniewest 9 months ago - 3 comments

#184 - instrain_compare clustering failure

Issue - State: closed - Opened by elisacaffrey 9 months ago - 5 comments

#183 - unable to lock file, errno = 37, error message = 'No locks available'

Issue - State: closed - Opened by 473021677 9 months ago - 2 comments

#182 - Errors for Merging splits and profiling genes

Issue - State: closed - Opened by 473021677 9 months ago - 2 comments

#180 - instrain profile step3

Issue - State: closed - Opened by Biofarmer 10 months ago - 8 comments

#179 - Questions about read coverage and breadth filtration.

Issue - State: closed - Opened by ChenTianYi99 11 months ago - 1 comment

#178 - inStrain compare: {genome} is in input {input} but not the provided stb file

Issue - State: closed - Opened by Sanrrone 11 months ago - 5 comments

#174 - inStrain Profile freeze - OSError: truncated file

Issue - State: closed - Opened by havi-rojer 11 months ago - 2 comments

#172 - what`s the meaning of the no data between the gene

Issue - State: closed - Opened by lori1996 11 months ago - 3 comments

#169 - Inconsistent order of columns in output file *_genome_info.tsv

Issue - State: open - Opened by yunkit 11 months ago - 1 comment
Labels: bug

#168 - calculations at the single-bacterial level

Issue - State: closed - Opened by dzxiaona 12 months ago - 1 comment

#167 - inStrain profile not profiling all genes

Issue - State: closed - Opened by rebeccasophiasalcedo 12 months ago - 7 comments

#166 - clarity regarding strain_clusters.tsv

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

#165 - about inStrain profile with KeyError: 'version'

Issue - State: closed - Opened by ZT-ls over 1 year ago - 11 comments

#164 - inStrain compare - output

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

#163 - DEBUG:no_length will not be considered as part of the genime

Issue - State: closed - Opened by Xiaoxin9115 over 1 year ago - 3 comments

#162 - Issue in statistical analysis of nucleotide diversity.

Issue - State: closed - Opened by ChenTianYi99 over 1 year ago - 2 comments

#161 - SNP calling naive question

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

#160 - genes with allele frequency differences

Issue - State: closed - Opened by haihao999 over 1 year ago - 2 comments

#159 - Enquiry about "codecs.py" and strain relative abundance

Issue - State: closed - Opened by jiangys30 over 1 year ago - 3 comments

#158 - Missing columns in "genome_info.tsv" output

Issue - State: closed - Opened by etd530 over 1 year ago - 3 comments

#156 - inStrain plot not generating plots 2 and 7

Issue - State: closed - Opened by cusoiv over 1 year ago - 9 comments
Labels: bug

#155 - How to calculate the pN/pS value of similar function genes

Issue - State: closed - Opened by haihao999 over 1 year ago - 1 comment

#154 - AttributeError: module 'numpy' has no attribute 'bool'.

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

#153 - a problem that has stations with different grain sizes

Issue - State: closed - Opened by haihao999 over 1 year ago

#152 - updata docker versin

Issue - State: closed - Opened by adobe7105 over 1 year ago - 2 comments

#151 - inStrain compare KeyError: 'covT'

Issue - State: closed - Opened by marina-vn over 1 year ago - 11 comments

#150 - Problem with installation using Docker

Issue - State: closed - Opened by camilagazolla almost 2 years ago - 1 comment

#149 - Same concept with amplicons?

Issue - State: closed - Opened by liamfitzstevens almost 2 years ago - 1 comment

#148 - inStrain compare sometimes hanging up

Issue - State: closed - Opened by cusoiv almost 2 years ago - 13 comments

#147 - isntallation problem

Issue - State: closed - Opened by Elennona almost 2 years ago - 1 comment

#146 - >8h for`Step 2. Profile scaffolds`

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

#145 - merging custom genomes with an existing genome database using drep "-extraW "

Issue - State: closed - Opened by yan1365 almost 2 years ago - 2 comments

#144 - Indexing error in IS_gene_info.tsv

Issue - State: closed - Opened by Winshipe almost 2 years ago - 3 comments

#143 - Optimal dRep %; run dRep on both isolates and MAGs?

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

#142 - Genome breadth of coverage

Issue - State: closed - Opened by Liuyuxinn almost 2 years ago - 1 comment

#141 - Troubleshooting inStrain profile Step 2. Profile scaffolds

Issue - State: closed - Opened by jmartin77777 almost 2 years ago - 3 comments

#140 - samtools left out of v1.7.1 pip installation

Issue - State: closed - Opened by rrohwer almost 2 years ago - 1 comment

#139 - Error trying to install pysam when installing instrain

Issue - State: closed - Opened by dzjian2 almost 2 years ago - 3 comments

#138 - -mb minimum breadth option in inStrain plot

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

#137 - pNpS calculations

Issue - State: closed - Opened by Riiiiiis almost 2 years ago - 9 comments

#136 - Dendrogram colours

Issue - State: closed - Opened by adijatj almost 2 years ago - 1 comment

#134 - making plots is failing although everything else finishes without error

Issue - State: closed - Opened by rrohwer about 2 years ago - 6 comments

#133 - instrain compare on multiple profiles

Issue - State: closed - Opened by adijatj about 2 years ago - 5 comments

#132 - conda/pip installations need phython <3.11

Issue - State: closed - Opened by rrohwer about 2 years ago - 2 comments
Labels: good first issue

#131 - retrieving data underneath plot #3 - read ANI distribution

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

#130 - missing genomes in genome_info.tsv files.

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

#129 - Update README.md

Pull Request - State: closed - Opened by alexcritschristoph about 2 years ago - 1 comment

#128 - Compare does not create plot 10

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

#127 - Trouble installing inStrain with Conda

Issue - State: closed - Opened by alipirani88 about 2 years ago - 2 comments

#125 - Is this method applicable to eukaryotes？

Issue - State: closed - Opened by haihao999 about 2 years ago - 1 comment

#124 - instrain profile flag "min_read_ani" not working?

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

#123 - to include or remove plasmids in reference genome databases?

Issue - State: closed - Opened by brittanysuttner about 2 years ago - 1 comment

#122 - FileNotFoundError: [Errno 2] No such file or directory: 'samtools'

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

#121 - Suppress Pandas FutureWarning

Pull Request - State: closed - Opened by vinisalazar over 2 years ago - 1 comment

#120 - Question about instrain

Issue - State: closed - Opened by SilasK over 2 years ago - 5 comments

#119 - inStrain compare: AssertionError: No scaffolds are shared amoung the IS

Issue - State: closed - Opened by celine77 over 2 years ago - 13 comments

#118 - Use bining data as ref-genome

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

#117 - Problem of false positive SNVs

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

#116 - Best practice to compare hundreds of samples

Issue - State: closed - Opened by zhaoc1 over 2 years ago - 2 comments

#115 - FutureWarning message of v1.6.3.

Issue - State: closed - Opened by zhaoc1 over 2 years ago - 2 comments
Labels: good first issue

#114 - Minor issue with argument orders for inStrain profile

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

#113 - ModuleNotFoundError: No module named 'numba'`

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

#110 - position in scaffold

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

#109 - inStrain compare key error when SNV Pooling

Issue - State: closed - Opened by szimmerman92 over 2 years ago - 4 comments
Labels: bug

#108 - Question: SNVs shared across samples

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