GitHub / theislab/single-cell-tutorial / commits
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
| SHA | Message | Author | Date | Stats |
|---|---|---|---|---|
| 12a86e12 | merge Merge pull request #109 from theislab/feature/note |
Lukas Heumos <l****s@p****t>
Committed by: GitHub <n****y@g****m> |
over 3 years ago | |
| 38409730 |
merge
Fix conflicts
Signed-off-by: zethson <l****s@p****t> |
zethson <l****s@p****t> | over 3 years ago | |
| aed1586d |
Adapt wording to PR feedback
Signed-off-by: zethson <l****s@p****t> |
zethson <l****s@p****t> | over 3 years ago | |
| f9a0abbc | Add a new line to the README warning |
Lukas Heumos <l****s@p****t>
Committed by: GitHub <n****y@g****m> |
over 3 years ago | |
| 796c8b6f |
Add missing full stop
Signed-off-by: zethson <l****s@p****t> |
zethson <l****s@p****t> | over 3 years ago | |
| c1f067f2 |
Add warning to refer to book
Signed-off-by: zethson <l****s@p****t> |
zethson <l****s@p****t> | over 3 years ago | |
| 48dc8e84 | merge Merge pull request #69 from herokoking/patch-1 |
MalteDLuecken <m****n@h****e>
Committed by: GitHub <n****y@g****m> |
about 5 years ago | |
| 272ab85b | Update sc_tutorial_environment.yml |
herokoking <3****g@u****m>
Committed by: GitHub <n****y@g****m> |
about 5 years ago | |
| 7ace03ab | merge Merge pull request #53 from lzhus/master |
MalteDLuecken <m****n@h****e>
Committed by: GitHub <n****y@g****m> |
over 5 years ago | |
| 7b5b3d73 | fix bug | Shen Ling <l****s@o****m> | over 5 years ago | |
| 0dbe8dfa | fix bug | Shen Ling <l****s@o****m> | almost 6 years ago | |
| 8168bcb9 | merge Merge pull request #47 from le-ander/master |
MalteDLuecken <m****n@h****e>
Committed by: GitHub <n****y@g****m> |
almost 6 years ago | |
| f10cbab0 | ping python package versions in dockerfile | le-ander <2****r@u****m> | almost 6 years ago | |
| 3d66fcfe | fix dockerfile | le-ander <2****r@u****m> | almost 6 years ago | |
| 204cf39d | merge Merge pull request #46 from le-ander/master |
MalteDLuecken <m****n@h****e>
Committed by: GitHub <n****y@g****m> |
almost 6 years ago | |
| d56a2248 | Add Dockerfile for sc-analysis Container | le-ander <2****r@u****m> | almost 6 years ago | |
| d2b8e1d3 | update leander's github link | LuckyMD <m****n@g****m> | over 6 years ago | |
| e787848c | add docker reference | LuckyMD <m****n@g****m> | over 6 years ago | |
| 6c270384 | updated install recommendations for mac | LuckyMD <m****n@g****m> | almost 7 years ago | |
| e3dbada7 | updated README with IRkernel instructions | LuckyMD <m****n@g****m> | almost 7 years ago | |
| c9e05bd3 | anndata2ri is on PyPI |
Philipp A <f****p@w****e>
Committed by: GitHub <n****y@g****m> |
almost 7 years ago | |
| 0ad826cf | updated how to find conda env directory in README | LuckyMD <m****n@g****m> | about 7 years ago | |
| ee0ac9dc | add F1000 prime recommendation badge | LuckyMD <m****n@g****m> | about 7 years ago | |
| 603e25fe | merge Merge pull request #19 from federicomarini/patch-1 |
MalteDLuecken <m****n@g****m>
Committed by: GitHub <n****y@g****m> |
about 7 years ago | |
| c7d0ac98 | Fixed folder name |
Federico Marini <m****f@u****e>
Committed by: GitHub <n****y@g****m> |
about 7 years ago | |
| ec9f2b03 | updated environment descriptions to use gprofiler-official instead of python-... | LuckyMD <m****n@i****e> | about 7 years ago | |
| 033b01b6 | added new case study with: new g:profiler package, scipy 1.3.0 compatibility,... | LuckyMD <m****n@i****e> | about 7 years ago | |
| 0937d8e3 | merge Merge pull request #16 from ttriche/patch-2 |
MalteDLuecken <m****n@g****m>
Committed by: GitHub <n****y@g****m> |
about 7 years ago | |
| 68e582ec | cleaner typo fix |
Tim Triche, Jr <t****e@g****m>
Committed by: GitHub <n****y@g****m> |
about 7 years ago | |
| 0dd33610 | fix formatting | LuckyMD <m****n@g****m> | over 7 years ago | |
| 92704dc6 | restructured readme | LuckyMD <m****n@g****m> | over 7 years ago | |
| e900539b | link image via google drive | LuckyMD <m****n@g****m> | over 7 years ago | |
| fc7f14ea | add a figure to the README | LuckyMD <m****n@g****m> | over 7 years ago | |
| 98970629 | went back to python>=3.5 in environment.yml file | LuckyMD <m****n@g****m> | over 7 years ago | |
| 164c6894 | added cmake, r-rngtools, and bioconductor-rhdf5lib from bioconda to environme... | LuckyMD <m****n@g****m> | over 7 years ago | |
| bd696068 | changed environment.yml file to limit to python 3.6 | LuckyMD <m****n@g****m> | over 7 years ago | |
| 4a61a9c0 | Updated AnnData version required |
MalteDLuecken <m****n@g****m>
Committed by: GitHub <n****y@g****m> |
over 7 years ago | |
| 981613e9 | updated notebook to use marker_gene_overlap function | LuckyMD <m****n@i****e> | over 7 years ago | |
| 62a2de9e | merge Merge branch 'master' of https://www.github.com/theislab/single-cell-tutorial | LuckyMD <m****n@i****e> | over 7 years ago | |
| af3bf0ef | added new notebook with sc.tl.embedding_density() and sc.pl.embedding_density() | LuckyMD <m****n@i****e> | over 7 years ago | |
| 918a5518 | alternative clustering in progress README | LuckyMD <m****n@g****m> | over 7 years ago | |
| 4fc76823 | merge Merge branch 'master' of https://www.github.com/theislab/single-cell-tutorial | LuckyMD <m****n@i****e> | over 7 years ago | |
| 3af54bdd | removed .libPaths() check | LuckyMD <m****n@i****e> | over 7 years ago | |
| b27cd637 | updated latest notebok README to include >= instead of > | LuckyMD <m****n@g****m> | over 7 years ago | |
| 99e741c5 | added README files for notebook releases | LuckyMD <m****n@g****m> | over 7 years ago | |
| 6ac4489d | updated naming of latest notebook | LuckyMD <m****n@g****m> | over 7 years ago | |
| 21c54384 | removed double old case study notebook | LuckyMD <m****n@g****m> | over 7 years ago | |
| bac6424e | added updated case study notebook with anndata2ri, pandas 0.24 compatability,... | LuckyMD <m****n@i****e> | over 7 years ago | |
| f3f76e07 | added reproducibility comments about svd_solver='arpack' | LuckyMD <m****n@g****m> | over 7 years ago | |
| 01b9c8fb | added download instructions for comparison dataset | LuckyMD <m****n@g****m> | over 7 years ago | |
| 5b0328f5 | added description comment to plot_hvgs.r file | LuckyMD <m****n@g****m> | over 7 years ago | |
| 5f7f3d79 | added plotting script for extended view figure 1, the HVG plot | LuckyMD <m****n@g****m> | over 7 years ago | |
| 3827bbb3 | changed HVG recommendation numbers in Case study old release | LuckyMD <m****n@g****m> | over 7 years ago | |
| ce97741a | added latest notebook folder and alternative clustering results folder and me... | LuckyMD <m****n@g****m> | over 7 years ago | |
| 5549caed | removed old file now renamed from old_releases | LuckyMD <m****n@g****m> | over 7 years ago | |
| bd183bfe | renamed old case study script | LuckyMD <m****n@g****m> | over 7 years ago | |
| 0a20c80e | added a README for the old_releases scripts | LuckyMD <m****n@g****m> | over 7 years ago | |
| 81a875c5 | updated title of manuscript and changed structure of repo | LuckyMD <m****n@g****m> | over 7 years ago | |
| ebfbb00f | updated structure of folder with latest and old versions of notebooks | LuckyMD <m****n@g****m> | over 7 years ago | |
| a33b78ab | added some additional code documentation to the case study | LuckyMD <m****n@g****m> | over 7 years ago | |
| 6aa85134 | fixed indenting in conda instructions for mac file again | LuckyMD <m****n@g****m> | over 7 years ago | |
| 4c36e7c2 | fixed indenting in conda instructions for mac file | LuckyMD <m****n@g****m> | over 7 years ago | |
| 92ff12cf | turned conda env instructions for mac into a markdown file rather than txt | LuckyMD <m****n@g****m> | over 7 years ago | |
| 2e349113 | merge Merge branch 'master' of https://github.com/theislab/single-cell-tutorial | LuckyMD <m****n@g****m> | over 7 years ago | |
| 192c44e4 | added conda env setup instructions for mac | LuckyMD <m****n@g****m> | over 7 years ago | |
| 4f8e8c54 | fixed list indents in README | LuckyMD <m****n@i****e> | over 7 years ago | |
| 856a3d05 | fixed typos and indented README.md lists | LuckyMD <m****n@i****e> | over 7 years ago | |
| e8733646 | merge merged README.md file with environment setup and data download | LuckyMD <m****n@i****e> | over 7 years ago | |
| f58f3909 | add instructions for setting up a conda environment and amended README to mat... | LuckyMD <m****n@i****e> | over 7 years ago | |
| bb791ddc | updated READEM with instructions on how to obtain the dataset | LuckyMD <m****n@g****m> | over 7 years ago | |
| cb5cbe44 | added pandas 0.24.0 warnings | LuckyMD <m****n@g****m> | over 7 years ago | |
| ba7f38e3 | added README warning about clusterExperiment package update naming convention... | LuckyMD <m****n@g****m> | over 7 years ago | |
| ddf5685a | better referencing of Haber et al paper | LuckyMD <m****n@g****m> | over 7 years ago | |
| 19acc99a | added better reference of Macosko et al. paper for cell cycle genes, and adde... | LuckyMD <m****n@g****m> | over 7 years ago | |
| bb7c6a21 | added scran as a requirement on the README | LuckyMD <m****n@g****m> | over 7 years ago | |
| b7bfb24a | reorganized repo to improve structure | LuckyMD <m****n@g****m> | over 7 years ago | |
| d29cbfd7 | updated the README to include notes for adapting the tutorial script, specifi... | LuckyMD <m****n@g****m> | over 7 years ago | |
| b9d20031 | updated requirements in README.md | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 409a4bb6 | updated the README to reflect plotting_scripts folder | LuckyMD <m****n@g****m> | almost 8 years ago | |
| b5348e4a | added figure plotting scripts | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 2c67bdaa | updated splatter script explanations and added a visualization | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 08a15891 | updated the README file | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 1fb14f7a | Cleaned up some comments and added further explanations for case study and su... | LuckyMD <m****n@g****m> | almost 8 years ago | |
| b49622a3 | added combat note | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 0a9c4d35 | added table of contents | LuckyMD <m****n@g****m> | almost 8 years ago | |
| dd26f5e7 | added timings to case study | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 0ad091fd | updated some typos | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 20154de6 | clarified data location and small comment improvements | LuckyMD <m****n@g****m> | almost 8 years ago | |
| f459c594 | Added jupyter notebook showing marker genes are detected in random data | LuckyMD <m****n@g****m> | almost 8 years ago | |
| edb08157 | Added the case study | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 970c7645 | updated the README | LuckyMD <m****n@g****m> | almost 8 years ago | |
| 18379448 | first commit | LuckyMD <m****n@g****m> | almost 8 years ago | |
| aceee511 | first commit | LuckyMD <m****n@g****m> | almost 8 years ago |