Commits · master · CNIO Bioinformatics Unit / bollito

Sep 13, 2022
- Add notice about move to GitHub · 0e0f17e1
  Tomás Di Domenico authored Sep 13, 2022
  
  0e0f17e1
- Re-add smaller images after repo cleanup · 55462b78
  Tomás Di Domenico authored Sep 13, 2022
  
  55462b78
Sep 08, 2022
- Get whitelist file using CI · ebd489c0
  Tomás Di Domenico authored Sep 08, 2022
  
  ebd489c0
Jul 20, 2022
- Change mem to mem_mb · d4f799f6
  Tomás Di Domenico authored Jul 20, 2022
  
  v1.0.5
  
  d4f799f6
Feb 23, 2022
- Fix report instructions · 8f9612b5
  Tomás Di Domenico authored Feb 23, 2022
  
  v1.0.4
  
  8f9612b5
- Update link to melanoma sample files. · 9f194cc4
  Coral Fustero-Torre authored Feb 23, 2022 and Tomás Di Domenico committed Feb 23, 2022
  
  9f194cc4
Feb 07, 2022
- Fix expression tables header. · fd6bd5ad
  Coral Fustero-Torre authored Feb 07, 2022 and Tomás Di Domenico committed Feb 07, 2022
```
closes #109
```
  fd6bd5ad
Feb 02, 2022
- Fix bad config reference in report (fixes #106 ) · 9532dd12
  Tomás Di Domenico authored Feb 02, 2022
  
  9532dd12
- Conda env cleanup · 45e64c71
  Tomás Di Domenico authored Feb 02, 2022
  
  45e64c71
Feb 01, 2022
- Modify multiqc's wrapper version · f4272c79
  Coral Fustero-Torre authored Feb 01, 2022
  
  f4272c79
Dec 15, 2021
- Correct bug in mitochondrial genes case format. Closes #105 · bdbeb365
  Coral Fustero-Torre authored Dec 15, 2021 and Tomás Di Domenico committed Dec 15, 2021
  
  bdbeb365
Nov 08, 2021
- Update README.md · 4c2eb3a5
  Coral Fustero-Torre authored Nov 08, 2021
  
  v1.0.0
  
  4c2eb3a5
Sep 14, 2021
- Update README authorship · 66a7e7b5
  Coral Fustero-Torre authored Sep 14, 2021
  
  66a7e7b5
Sep 10, 2021
- Add benchmarking and LISI sections to README · 7fe0f0a5
  Luis García Jimeno authored Sep 10, 2021 and Tomás Di Domenico committed Sep 10, 2021
  
  7fe0f0a5
Sep 08, 2021
- Set r-base version. · 16053d61
  Coral Fustero-Torre authored Sep 08, 2021
  
  16053d61
Sep 07, 2021
- Fix bug in clustree functional calculation. · 77edbff4
  Coral Fustero-Torre authored Sep 07, 2021 and Tomás Di Domenico committed Sep 07, 2021
  
  77edbff4
- Fix vision calculation for integrated data. · e5218170
  Coral Fustero-Torre authored Sep 07, 2021
  
  e5218170
- Add Local Inverse Simpson’s Index (LISI) computation for all variables of interest. · 62ae564a
  Coral Fustero-Torre authored Sep 07, 2021 and Tomás Di Domenico committed Sep 07, 2021
  
  62ae564a
Sep 02, 2021
- Add creation of AnnData file from Seurat object · d4b2a6b8
  Luis García Jimeno authored Sep 02, 2021 and Tomás Di Domenico committed Sep 02, 2021
  
  d4b2a6b8
- Add a parameter to run the PCA using all or variable features only. · 4cbd54d5
  Coral Fustero-Torre authored Sep 02, 2021 and Tomás Di Domenico committed Sep 02, 2021
  
  4cbd54d5
Aug 30, 2021
- Allow the analysis of single (integrated/merged) samples · 87829456
  Luis García Jimeno authored Aug 30, 2021 and Tomás Di Domenico committed Aug 30, 2021
  
  87829456
Jul 28, 2021
- Correction - Complete seurat object is used to get the clustering UMAP plots. · af18b86d
  Luis García Jimeno authored Jul 28, 2021
  
  af18b86d
Jul 19, 2021

Add to the config.yaml the option write_table. If write_table False, bollito... · c5aed701

ktroule authored Jul 19, 2021

Add to the config.yaml the option write_table. If write_table False, bollito won't write the tsv matrices. This is can be of help on the extreme case where the number of cells is too high and R cannot write the count matrices as tsv due to memory issues

c5aed701

Jul 14, 2021
- Add DownSample to 50K to calculate Silhouette · 0746f5e2
  ktroule authored Jul 14, 2021
  
  0746f5e2
Jun 11, 2021
- Add matrix package to seurat environments · 88ebd6b7
  Coral Fustero-Torre authored Jun 11, 2021
  
  88ebd6b7
May 20, 2021
- Update documentation · 56c0fc17
  Luis García Jimeno authored May 20, 2021 and Tomás Di Domenico committed May 20, 2021
  
  56c0fc17
May 13, 2021
- Update melanoma tutorial · d5d5c905
  Coral Fustero-Torre authored May 13, 2021 and Tomás Di Domenico committed May 13, 2021
  
  d5d5c905
- Correct bug when adding velocity matrices to the seurat object. · 50cc43e7
  Coral Fustero-Torre authored May 13, 2021
  
  50cc43e7
May 11, 2021
- Add LICENSE · 3d0fbafe
  Tomás Di Domenico authored May 11, 2021
  
  3d0fbafe
May 06, 2021
- Eliminate selected_res parameter from the seurad_degs section in config. · 89279c1f
  Coral Fustero-Torre authored May 06, 2021
  
  89279c1f
May 04, 2021
- DE step now accepts multiple metadata columns, closes #102 . · d6a36347
  Coral Fustero-Torre authored May 04, 2021 and Tomás Di Domenico committed May 04, 2021
  
  d6a36347
Apr 29, 2021
- Export normalized matrix instead of the scaled matrix. Closes #101 · f84424d0
  Coral Fustero-Torre authored Apr 29, 2021 and Tomás Di Domenico committed Apr 29, 2021
  
  f84424d0
- Aply counts/feature min and max filters at once. Closes #97 · 92b04b2b
  Coral Fustero-Torre authored Apr 29, 2021
  
  92b04b2b
- Allow cell cycle regression during the integration step. Closes #99 and #100 · b519b446
  Coral Fustero-Torre authored Apr 29, 2021 and Tomás Di Domenico committed Apr 29, 2021
  
  b519b446
Apr 26, 2021
- Fix environments · 35f1dee1
  Luis García Jimeno authored Apr 26, 2021 and Tomás Di Domenico committed Apr 26, 2021
  
  35f1dee1
Mar 16, 2021
- Update step2.1_filter.R · 2855fda4
  Luis García Jimeno authored Mar 16, 2021
  
  2855fda4
- Update step2.5_seurat_merge.R · ebd8a27a
  Luis García Jimeno authored Mar 16, 2021
  
  ebd8a27a
- Update step1_qc.R · 5d056c01
  Luis García Jimeno authored Mar 16, 2021
  
  5d056c01
Mar 04, 2021
- Heatmap and QC plots fixed. · dd250c0a
  Luis García Jimeno authored Mar 04, 2021
  
  dd250c0a
Feb 10, 2021
- Modify marker genes heatmap Closes #90 · fa3fe7cf
  Coral Fustero-Torre authored Feb 10, 2021
  
  fa3fe7cf