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montilab

13 indexed repositories · View on GitHub

hypeR
An R Package for Geneset Enrichment Workflows

R · 79 stars
pipeliner
A flexible Nextflow-based framework for the definition of sequencing data processing pipelines

Nextflow · 44 stars
nf-gwas-pipeline
A Nextflow Genome-Wide Association Study (GWAS) Pipeline

R · 36 stars
BS831
Course Materials for Genomics Data Mining

HTML · 22 stars
chen_et_al_brca_atlas
Integrated scRNAseq atlas of Breast Cancer

HTML · 3 stars
OmicSignature

R · 3 stars
SigRepo
SigRepo: An R package for storing and processing omic signatures

R · 3 stars
yQTLpipeline

R · 1 star
hypeR-GEM
A R Package For Connecting Metabolic Signatures to Enzyme-coding Genes

R · 1 star
sigrecon
Benchmarking tasks for the recontextualization of gene expression signatures

R · 1 star
hypeR-db
A hypeR repository for relational and flat genesets

0 stars
RSNet
Resampling-based Network Structure Inference

R · 0 stars
SigRepo_Server
Server Architecture of SigRepo Database

HTML · 0 stars

Beginner friendly Everything

Open All

SignatureSearch needs to be "optimized" Open

enhancement ready

montilab/SigRepo#231 · 1 comment · 2 assignees · Opened Sep 20, 2026
signatureSearch should work with regular expressions Open

enhancement ready

montilab/SigRepo#230 · 2 assignees · Opened Sep 20, 2026
macOS: new RMySQL (>= 0.11.2) cannot connect — TLS certificate verification failure Open

bug ready

montilab/SigRepo#229 · 1 assignee · Opened Sep 20, 2026
OmicSignature: incorrect signature creation Open

data-quality

montilab/SigRepo_Server#97 · 1 assignee · Opened Sep 19, 2026
Manage Access on the Signature tab is non-functional: no grant ever reaches the database Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 62/100

montilab/SigRepo_Server#96 · Opened Sep 19, 2026
signature view Open

enhancement ready

montilab/SigRepo_Server#95 · 2 comments · 1 assignee · Opened Sep 19, 2026
6 public signatures have no feature rows: getSignature() fails with "Signature is empty" Open

bug data-quality ready

montilab/SigRepo_Server#89 · 1 comment · 2 assignees · Opened Sep 17, 2026
TCGA RNA-seq aging signatures are stored unthresholded (signature table == difexp table) Open

bug data-quality ready

montilab/SigRepo#227 · 2 comments · 1 assignee · Opened Sep 17, 2026
Run Shiny compares in a forked child process so memory is released and other sessions are not blocked Open

blocked enhancement

Difficulty 4/5 3-5 days Newbie friendliness 68/100

montilab/SigRepo_Server#88 · 1 comment · Opened Sep 17, 2026
Dev Branch Instance on montilab Open

enhancement ready

Difficulty 4/5 3-5 days Newbie friendliness 35/100

montilab/SigRepo_Server#84 · Opened Sep 17, 2026
annotate vignette Open

documentation ready

montilab/SigRepo#225 · 1 assignee · Opened Sep 17, 2026
Signatures lacking symbols in difexp Open

data-quality enhancement ready

montilab/SigRepo#224 · 1 assignee · Opened Sep 17, 2026
compare_signatures_vignette Open

documentation ready

Difficulty 3/5 1-2 days Newbie friendliness 68/100

montilab/SigRepo#222 · Opened Sep 17, 2026
Rebuild the Shiny Annotate tab on SigRepo::runHypeR() Open

enhancement ready

Difficulty 5/5 Over a week Newbie friendliness 30/100

montilab/SigRepo_Server#83 · Opened Sep 15, 2026
hypeR-GEM Open

enhancement ready

montilab/SigRepo#211 · 1 assignee · Opened Sep 14, 2026
R-Client HypeR Review Open

bug ready

montilab/SigRepo#198 · 1 assignee · Opened Sep 11, 2026
RefMet "versioning" Open

montilab/hypeR-GEM#7 · 2 assignees · Opened Aug 22, 2026
Reduce genesets function Open

montilab/hypeR-GEM#6 · 1 comment · 2 assignees · Opened Aug 21, 2026
Gene background should have a default Open

montilab/hypeR-GEM#5 · 1 assignee · Opened Aug 21, 2026
Support unary (uni-directional) and categorical (>2 level) signatures in compare_omic_signatures() Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

montilab/OmicSignature#50 · 1 comment · Opened Jul 17, 2026
Idea Proposal: AI Endpoints Brainstorm Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 38/100

montilab/SigRepo#180 · Opened Jul 2, 2026
Improve KS plot Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

montilab/hypeR#73 · 1 comment · Opened Jul 1, 2026
Feature request: "hybrid" bootstrap strategy for the differential connectivity function Open

Difficulty 4/5 3-5 days Newbie friendliness 55/100

montilab/RSNet#4 · Opened Jul 1, 2026
Idea Proposal: Report feature in OmicSignature Open

documentation enhancement

montilab/OmicSignature#33 · 1 assignee · Opened Jun 29, 2026
Error in diff_centrality when shuffle_method = bootstrap Open

Difficulty 3/5 1-2 days Newbie friendliness 62/100

montilab/RSNet#3 · Opened Jun 29, 2026
JOSS feedback: implement open-source practices Open

montilab/RSNet#2 · 1 comment · 1 assignee · Opened Jun 29, 2026
AI-supported signature ingestion Open

idea needs-decision

montilab/SigRepo#179 · 2 assignees · Opened Jun 29, 2026
Design and implement agent-facing SigRepo API endpoints for signature workflows Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 38/100

montilab/SigRepo#178 · Opened Jun 18, 2026
Design and prototype LLM-based annotation for signatures and signature collections Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 35/100

montilab/SigRepo#177 · 1 comment · Opened Jun 18, 2026
HypeR integration into SigRepo R-Client Open

enhancement ready

montilab/SigRepo#176 · 2 comments · 1 assignee · Opened Jun 17, 2026
Agent-facing Endpoints Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#174 · Opened Jun 9, 2026
Reference workflows Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#173 · Opened Jun 9, 2026
Beyond signature collections Open

idea needs-decision

montilab/SigRepo#172 · 1 assignee · Opened Jun 4, 2026
Connect to MetaboAnalyst Open

idea needs-decision

montilab/SigRepo#171 · 2 comments · 1 assignee · Opened Jun 4, 2026
hypeR-GEM-based annotation Open

enhancement ready

montilab/SigRepo#170 · 1 assignee · Opened Jun 4, 2026
methylomics Integration Open

enhancement needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#169 · Opened Jun 4, 2026
unique for probe id and gorup label Open

enhancement ready

Difficulty 3/5 1-2 days Newbie friendliness 48/100

montilab/SigRepo_Server#24 · Opened May 28, 2026
LLM-based signature list annotation Open

idea needs-decision

montilab/SigRepo#166 · 1 comment · 2 assignees · Opened May 24, 2026
categorical signature enrichment workflow Open

enhancement needs-decision

Difficulty 5/5 Over a week Newbie friendliness 45/100

montilab/SigRepo#161 · Opened May 14, 2026
Annotate_Fix Open

enhancement needs-decision

Difficulty 3/5 1-2 days Newbie friendliness 35/100

montilab/SigRepo_Server#16 · Opened Apr 13, 2026
code complexity Open

enhancement ready

Difficulty 4/5 3-5 days Newbie friendliness 35/100

montilab/SigRepo#134 · Opened Dec 9, 2025
Connect to GeneAgent Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#88 · Opened Oct 29, 2025
Connect to signatureSearch Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#83 · Opened Oct 24, 2025
Connect to CORESH Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 25/100

montilab/SigRepo#82 · Opened Oct 24, 2025
LibreChat Open

idea needs-decision

Difficulty 5/5 Over a week Newbie friendliness 15/100

montilab/SigRepo#79 · Opened Oct 22, 2025
Omics Type: Methylomics Open

enhancement needs-decision

Difficulty 5/5 Over a week Newbie friendliness 20/100

montilab/SigRepo#63 · 2 comments · Opened Oct 9, 2025
shinyjs hidden toggle bug Open

bug needs-decision

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

montilab/SigRepo_Server#7 · Opened Sep 29, 2025
Signature Tab Open

enhancement needs-decision

Difficulty 3/5 1-2 days Newbie friendliness 35/100

montilab/SigRepo_Server#4 · Opened Sep 25, 2025
Input format checks Open

montilab/OmicSignature#18 · 1 comment · 1 assignee · Opened Aug 27, 2025
Snakemake pipeline Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

montilab/chen_et_al_brca_atlas#6 · 2 comments · Opened Jun 11, 2025

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