Owner

AlexsLemonade

36 indexed repositories · View on GitHub

refinebio
Refine.bio harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scienti...

Python · 135 stars
training-modules
A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.

HTML · 77 stars
scpca-nf
scpca-nf is the Nextflow workflow for processing Single-cell Pediatric Cancer Atlas Portal data

R · 18 stars
OpenScPCA-analysis
An open, collaborative project to analyze data from the Single-cell Pediatric Cancer Atlas (ScPCA) Portal

HTML · 16 stars
refinebio-examples
Example workflows for refine.bio data

HTML · 11 stars
refinebio-frontend
Frontend app for refine.bio

JavaScript · 7 stars
exrcise
Selectively Excise Code Chunks for Exercises

R · 4 stars
scpca-portal
Single-cell Pediatric Cancer Atlas Portal is a growing database of uniformly processed single-cell data from pediatric cancer tumors and ...

JavaScript · 4 stars
cranlock
Lock our R dependencies to specific versions.

Python · 2 stars
ScPCAr
An R package for interacting with the ScPCA Portal API

R · 2 stars
OpenScPCA-nf
A workflow for running OpenScPCA analysis modules

R · 2 stars
refinebio-design
Design files and resources for refine.bio

Python · 1 star
scRNA-seq_sandbox
Exploring some scRNA-seq methodologies, not a full-fledged pipeline ready for use

R · 1 star
refinebio-docs
User Documentation for refine.bio

1 star
fancySVD
Only the IterativeSVD algorithm from iskandr/fancyimpute to make dependency resolution easier.

Python · 1 star
refinebio-py
A python client for the refine.bio API.

Python · 1 star
resources-portal

Python · 1 star
refinebio-web
Refinebio Web

JavaScript · 1 star
scpcaTools

R · 1 star
reproducible-research
Repository for Reproducible Research Practices Training Workshop

HTML · 1 star
16 more repositories live on View on GitHub

Open All

1063 open issues indexed

More dplyr love Open

AlexsLemonade/ccdl_header#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Better color scheme Open

AlexsLemonade/ccdl_header#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use SVG rather than PNG Open

AlexsLemonade/ccdl_header#5 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[human_missingness] Make human_missingness scripts generalized to all species Open

AlexsLemonade/compendium-processing#7 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Construct "masked" zebrafish matrix for use as gold standard for imputation challenge Open

AlexsLemonade/compendium-processing#10 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Running list of things to explore/validate in usability evals/user research Open

user research areas

AlexsLemonade/refinebio-design#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Connect to Vercel and set up environenment variables Open

AlexsLemonade/refinebio-design#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing Open

UXR

AlexsLemonade/refinebio-design#41 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing: Write script/test plan Open

UXR

AlexsLemonade/refinebio-design#42 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing: Setup Calendly Link Open

UXR

AlexsLemonade/refinebio-design#43 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing: Recruitment Criteria and Strategy Open

UXR

AlexsLemonade/refinebio-design#44 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing: Recuitment Copy Open

UXR

AlexsLemonade/refinebio-design#45 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
testing: Participant Incentive Open

UXR

AlexsLemonade/refinebio-design#46 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add installation of packages for all the post-processing scripts to Dockerfile Open

AlexsLemonade/scRNA-seq_sandbox#9 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Cell-type classification for tag-based scRNA-seq Open

AlexsLemonade/scRNA-seq_sandbox#18 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Differential expression analysis for scRNA-seq Open

AlexsLemonade/scRNA-seq_sandbox#19 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Filtering defaults for 10X Open

AlexsLemonade/scRNA-seq_sandbox#26 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Make Tabula Muris run steps for on aws more clear and reproducible Open

AlexsLemonade/scRNA-seq_sandbox#28 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Look into doublet finder algorithms Open

AlexsLemonade/scRNA-seq_sandbox#31 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Run scvi on these datasets Open

AlexsLemonade/scRNA-seq_sandbox#32 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Feature idea: Allow some code a block to be retained/uncommented Open

enhancement

AlexsLemonade/exrcise#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
remove reliance on knitr:::parse_params() Open

AlexsLemonade/exrcise#6 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Remove exrcsise-specific tags Open

enhancement

AlexsLemonade/exrcise#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow manually editing the versions.tsv file Open

AlexsLemonade/cranlock#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add the ability to pin dependencies for Bioconductor packages Open

AlexsLemonade/cranlock#3 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[Feature idea] Display what percentage of an experiment's samples we've processed Open

backlog design input exploration idea

AlexsLemonade/refinebio-frontend#463 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Let's Make Our Pagespeed Score Green! Open

backlog seo speed

AlexsLemonade/refinebio-frontend#553 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Can we support "AND" and "OR" logical operators in search? Open

exploration

AlexsLemonade/refinebio-frontend#604 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add a virtual map with pins of everywhere that we've had a user download from Open

AlexsLemonade/refinebio-frontend#642 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Consider adding a styleguide Open

maintainability

AlexsLemonade/refinebio-frontend#643 · 1 comment · 1 reaction · 1 assignee · Indexed Sep 14, 2026
Use react-spring in compendia animation Open

enhancement good first issue

AlexsLemonade/refinebio-frontend#665 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
[Feature Idea] Show list of related experiments Open

exploration idea seo

AlexsLemonade/refinebio-frontend#686 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Samples Table: Add filter field on each column Open

exploration in design new-feature

AlexsLemonade/refinebio-frontend#710 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Allow sending multiple words on elastic search parameters Open

good first issue

AlexsLemonade/refinebio-frontend#719 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Request browserstack licence for browser testing Open

AlexsLemonade/refinebio-frontend#725 · 1 comment · 1 reaction · 1 assignee · Indexed Sep 14, 2026
Dashboard Architecture: Current Phase Open

dashboard

AlexsLemonade/refinebio-frontend#729 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026
Dashboard Tweak: change order in which lines are drawn Open

dashboard easy win nice to have

AlexsLemonade/refinebio-frontend#730 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Display 'Running jobs by volume' over time Open

dashboard exploration new-feature relies on backend

AlexsLemonade/refinebio-frontend#734 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Smooth executive dashboard numbers / hr Open

dashboard

AlexsLemonade/refinebio-frontend#737 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Explore "Undo" adding to dataset feature Open

exploration

AlexsLemonade/refinebio-frontend#800 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improve social media previews of refine.bio Open

seo

AlexsLemonade/refinebio-frontend#852 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Bug on dataset page when removing an organism Open

bug

AlexsLemonade/refinebio-frontend#854 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use NextJS engine to generate the sitemap Open

seo

AlexsLemonade/refinebio-frontend#863 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Add sample pages to the sitemap Open

design input exploration seo

AlexsLemonade/refinebio-frontend#874 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Improve mobile device detection on the server side Open

seo

AlexsLemonade/refinebio-frontend#875 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use links in filters and pagination of the search page Open

seo

AlexsLemonade/refinebio-frontend#879 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Use an API endpoint to post messages to slack and hide the webhook url Open

AlexsLemonade/refinebio-frontend#884 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Show more states besides processing on the one-click experiment download Open

AlexsLemonade/refinebio-frontend#888 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Experiment Page returning 502 status code Open

AlexsLemonade/refinebio-frontend#920 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 14, 2026
Sample processing modal should include Ensembl release for RNA-seq samples Open

AlexsLemonade/refinebio-frontend#923 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 14, 2026

AlexsLemonade

Get new issues in your inbox