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ncbi/EvoGeneX
Are equal replicate numbers still required?

Hello! Thank you so much for your work on EvoGeneX! It is a very exciting and helpful program! Are equal numbers of replicates for each species still required to run EvoGeneX? I have one species with ...
  • mtswanson2017
  • 5
  • Opened 
    on Dec 15, 2025
  • #9

ncbi/tree-tool
[Draft] New Issue in ncbi/tree-tool

This is a draft issue created to gather additional information for a future actionable task or bug report. Please provide more details about the problem, enhancement, or task you wish to address in this ...
  • tumtee46-png
  • Opened 
    on Nov 9, 2025
  • #5

ncbi/tree-tool
Caki

  • tumtee46-png
  • Opened 
    on Nov 9, 2025
  • #4

ncbi/EvoGeneX
EvoGeneX R package installation fails - missing C++ function implementations

Issue Description The EvoGeneX R package cannot be installed due to missing C++ function implementations, resulting in undefined reference errors during compilation. Environment Details - Operating ...
  • yaaraneumeier
  • 2
  • Opened 
    on May 26, 2025
  • #6

ncbi/GeneSigNet
ValueError: You are using LassoLarsIC in the case where the number of samples is smaller than the number of features. In this setting, getting a good estimate for the variance of the noise is not possible. Provide an estimate of the noise variance in the constructor.

Hi, I ve been trying to use GeneSigNet for a while now, and I keep getting this error, and I am using the Gene_Expression_Simulated_Data.csv and Signature_Exposure_Simulated_Data.csv you provided. I ll ...
  • FerTalavera
  • Opened 
    on Nov 24, 2024
  • #1

ncbi/clinvar
ClinVar API not returning the correct last_evaluated date for germline classification

Hello, we use in our project the following API: https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi? db=clinvar api_key= which returns an xml. For the xml tag: germline_classification = last_evaluated ...
  • daianatoader
  • Opened 
    on Apr 11, 2024
  • #8

ncbi/clinvar
Validation of json submissions fails with error: 'clinvarDeletion' is a required property

Hello! I m curating a repository that coverts text files submissions files (Variants and Casedata files - csv or tsv to json submission objects and I have some tests that started failing as soon as I ve ...
  • northwestwitch
  • 1
  • Opened 
    on Mar 14, 2024
  • #7

ncbi/clinvar
VCF versioning, changelogs, documentation

Q1. Could you please clarify a recent change to the VCF file? There was a recent (as far as I can tell) undocumented change to the VCF format - it appears that recently the INFO field CLNREVSTAT - ClinVar ...
  • davmlaw
  • Opened 
    on Feb 12, 2024
  • #6

ncbi/clinvar
Web site broken link to VCF

On this page: https://www.ncbi.nlm.nih.gov/clinvar/docs/maintenance_use/ There is a broken link to VCFs: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf/ Should be https://ftp.ncbi.nih.gov/pub/clinvar/vcf_GRCh37/ ...
  • davmlaw
  • 1
  • Opened 
    on Feb 12, 2024
  • #5

ncbi/clinvar
Issue with E-utilities

When I use esummary, such as in this case https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=clinvar id=65533 I get an apparently broken XML eSummaryResult ERROR NCBI C++ Exception: ...
  • atturk
  • Opened 
    on Jan 30, 2024
  • #4
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