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Merck

34 indexed repositories · View on GitHub

BioPhi
BioPhi is an open-source antibody design platform. It features methods for automated antibody humanization (Sapiens), humanness evaluatio...

Python · 265 stars
deepbgc
BGC Detection and Classification Using Deep Learning

Jupyter Notebook · 161 stars
Halyard
Halyard is an extremely horizontally scalable Triplestore with support for Named Graphs, designed for integration of extremely large Sema...

Java · 114 stars
r2rtf
Easily Create Production-Ready Rich Text Format (RTF) Table and Figure

R · 85 stars
Sapiens
Sapiens is a human antibody language model based on BERT.

Jupyter Notebook · 80 stars
matcher
Matcher is a tool for understanding how chemical structure optimization problems have been solved. Matcher enables deep control over sear...

Python · 71 stars
DeepNeuralNet-QSAR

Python · 66 stars
rdf2x
RDF2X converts big RDF datasets to the relational database model, CSV, JSON and ElasticSearch.

Java · 57 stars
Line-of-Therapy-Algorithm
This is the Line of Therapy Algorithm, as described in the paper "Temporal phenotyping by mining healthcare data to derive lines of thera...

Python · 39 stars
simtrial
Clinical trial simulation for time-to-event endpoints

R · 39 stars
PepSeA

Python · 35 stars
gsDesign2
Group Sequential Design Under Non-Proportional Hazards

R · 34 stars
pkglite
Compact Package Representations

R · 31 stars
metalite.ae
An R package for standard adverse events analysis

R · 27 stars
sonar-r-plugin
Adds support for R language into SonarQube. It uses output from lintr tool which is processed by the plugin and uploaded into SonarQube s...

Java · 26 stars
forestly
Interactive forest plot for adverse events analysis

R · 22 stars
metalite
An R package to create metadata structure for ADaM data analysis and reporting

R · 18 stars
pmpo
Probabilistic Multi-Parameter Optimization (pMPO)

Python · 17 stars
mRNAid

Jupyter Notebook · 17 stars
AbLEF
Antibody Langauge Ensemble Fusion - fuses antibody structural ensemble and language representation for property prediction

Python · 14 stars
14 more repositories live on View on GitHub

Beginner friendly Everything

Open All

Serious AE listing is not presented while it is included in the metadata Open

Merck/forestly#154 · 1 assignee · Opened Sep 18, 2026
format_ae_specific fails in single group tables Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

Merck/metalite.ae#254 · Opened Sep 17, 2026
Add `ae_listing_label = ...` to `prepare_ae_forestly()` Open

Merck/forestly#152 · 1 assignee · Opened Sep 17, 2026
`to_integer()` removes column `spending_time` from the bound table Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

Merck/gsDesign2#675 · Opened Sep 14, 2026
A lot of if-else in `format_ae_listing()` Open

Merck/forestly#148 · 1 comment · 1 assignee · Opened Sep 11, 2026
Running time optimization Open

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

Merck/forestly#147 · 1 comment · Opened Sep 11, 2026
Change `gs_cp(theta = ...)` from cumulative treatment effect to incremental treatment effect Open

Merck/gsDesign2#670 · 1 assignee · Opened Sep 9, 2026
Add minimum median follow-up time at time of design Open

Merck/gsDesign2#669 · 1 assignee · Opened Sep 9, 2026
collect_n_subject() should use an explicit rounding policy at display boundaries Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

Merck/metalite#184 · Opened Sep 8, 2026
Clinical-reporting vignettes should use an explicit rounding policy Open

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

Merck/r2rtf#296 · Opened Sep 8, 2026
[BUG] Rounding does not follow round-half-away-from-zero on decimal ties and displayed values show negative zeros Open

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

Merck/metalite.ae#249 · 1 comment · Opened Sep 6, 2026
Simplify lt.R using lt predicate selectors and spanner auto-reorder (next lt release) Open

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

Merck/simtrial#373 · Opened Sep 3, 2026
Re-org pkgdown website Open

Merck/boxly#55 · 1 assignee · Opened Aug 28, 2026
Consider adding functionality to transform `theta` for gs_cp functions between cumulative and incremental drift Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

Merck/gsDesign2#668 · Opened Aug 26, 2026
Typo in documentation for gs_cp_npe1.R Open

Difficulty 1/5 Under an hour Newbie friendliness 92/100

Merck/gsDesign2#665 · Opened Aug 25, 2026
Fully remove gt dependency after the as_gt() deprecation period Open

Difficulty 4/5 3-5 days Newbie friendliness 65/100

Merck/gsDesign2#663 · 1 reaction · Opened Aug 21, 2026
Fix RTF download issues Open

Merck/metalite.ae#236 · 2 comments · 1 assignee · Opened Aug 13, 2026
Improvement of `format_ae_listing()` Open

Difficulty 3/5 1-2 days Newbie friendliness 65/100

Merck/forestly#138 · Opened Jun 29, 2026
Error from the `var =...` in `define_population` and `define_observation` Open

Difficulty 3/5 1-2 days Newbie friendliness 58/100

Merck/forestly#137 · Opened Jun 29, 2026
Tasks are waiting in queue... Open

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

Merck/BioPhi#89 · Opened Jun 24, 2026
Vectorize grouping variables inside of `define_population` and `define_observation` Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

Merck/metalite#182 · Opened Jun 16, 2026
Release Version V0.2.6 Open

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

Merck/pkglite#65 · Opened Jun 8, 2026
Create ADEXSUM dataset Open

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

Merck/metalite.sl#136 · Opened May 28, 2026
Why do we have `display_stat = ...` in `format_disposition()`? Open

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

Merck/metalite.sl#135 · Opened May 28, 2026
OASis local set prevalence threshold Open

Difficulty 2/5 1-3 hours Newbie friendliness 57/100

Merck/BioPhi#87 · Opened Apr 29, 2026
Capability to config number of rows of each page Open

enhancement

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

Merck/r2rtf#290 · Opened Apr 21, 2026
Saving ggplot object as rtf Open

question

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

Merck/r2rtf#289 · 1 comment · Opened Apr 17, 2026
OASis prevalence threshold for custom Open

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

Merck/BioPhi#86 · Opened Apr 17, 2026
Cause an error when non-existing columns are selected in `collect_observation_record(var=...)` Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

Merck/metalite#181 · Opened Apr 13, 2026
`observation` cannot be extracted when `population` and `observation` names are the same Open

Difficulty 3/5 1-2 days Newbie friendliness 52/100

Merck/metalite#180 · Opened Apr 13, 2026
generate_corr() produces invalid correlation matrix for k > 2 analyses Open

Merck/wpgsd#48 · 1 assignee · Opened Mar 13, 2026
Re-do group sequential vignette using graphicalMCP Open

Merck/gMCPLite#44 · 1 assignee · Opened Mar 5, 2026
bootstrap加载优化 Open

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

Merck/BioPhi#85 · Opened Mar 5, 2026
Port user-definable graphicalMCP magic number to add to gMCPLite graphs Open

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

Merck/gMCPLite#42 · Opened Feb 26, 2026
The server is waiting indefinitely Open

Difficulty 4/5 3-5 days Newbie friendliness 15/100

Merck/BioPhi#84 · Opened Jan 27, 2026
Gray line in treatment labels for longer labels Open

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

Merck/forestly#111 · Opened Dec 19, 2025
Harmonize the multiple versions links Open

bug help wanted

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

Merck/gMCPShiny#9 · 1 comment · Opened Nov 5, 2025
The BioPhi server is not working Open

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

Merck/BioPhi#83 · Opened Nov 3, 2025
Error: [Errno 24] Too many open files: '/tmp/tmps9os6anr.fasta' Open

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

Merck/BioPhi#82 · 2 comments · Opened Oct 26, 2025
BioPhi failed with TypeError: predict_scores() got an unexpected keyword argument 'model_version' Open

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

Merck/BioPhi#81 · 1 comment · Opened Oct 23, 2025
The biophi server is not working! Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#80 · Opened Oct 21, 2025
Weird row number in the interactive baseline characteristic table when drill down to AE subgroup Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

Merck/metalite.sl#123 · 1 comment · Opened Oct 20, 2025
A bug of `prepare_boxly` Open

Merck/boxly#45 · 1 comment · 1 assignee · Opened Oct 17, 2025
Update `react_base_char` by incorporating population and observation from both baseline characteristics table and AE specific table Open

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

Merck/metalite.sl#120 · 1 comment · Opened Oct 17, 2025
Add `var = ...` to `define_population` and `define_observation` Open

Merck/forestly#107 · 1 assignee · Opened Oct 17, 2025
Cannot get image from quay.io Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#79 · 3 comments · Opened Oct 16, 2025
Error: [Errno 12] Cannot allocate memory Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/BioPhi#78 · 1 comment · Opened Oct 15, 2025
Add a vignette introducing how to custom listing in interactive disposition tables Open

Merck/metalite.sl#115 · 1 assignee · Opened Oct 13, 2025
Installing DeepBGC for pipeline integration Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

Merck/deepbgc#104 · Opened Oct 3, 2025
Allow users to disable the drill down to AE tables when reviewing interactive baseline characteristic table Open

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

Merck/metalite.sl#110 · 1 comment · Opened Oct 2, 2025

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