Last updated: 2022-10-03

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Knit directory: BAUH_2020_MND-single-cell/analysis/

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These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (public/index.html) files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view the files as they were in that past version.

File Version Author Date Message
html ea94c29 cazodi 2022-09-30 push fastqc
html b38f276 cazodi 2022-09-29 pilot 4 lenti fastQC
html 927ff1d cazodi 2022-07-16 pilot 4
Rmd feed601 cazodi 2022-05-03 figures for chris about celltype abundance
html feed601 cazodi 2022-05-03 figures for chris about celltype abundance
html 8ac0d8a cazodi 2022-03-30 update rmarkdown
Rmd d01f3b8 cazodi 2022-03-30 testing snp filtering for vireo
html d01f3b8 cazodi 2022-03-30 testing snp filtering for vireo
html 2c95e3b cazodi 2022-03-09 add stats to demulxiplexing results
Rmd c683543 cazodi 2022-03-09 updated c5 lenti barcode analysis and donor assignment comparisons
html c683543 cazodi 2022-03-09 updated c5 lenti barcode analysis and donor assignment comparisons
Rmd 77c6459 cazodi 2022-03-02 add joint cell calling results
html 77c6459 cazodi 2022-03-02 add joint cell calling results
html 3f19b81 cazodi 2022-03-01 update index
Rmd 9eb9fcc cazodi 2022-03-01 add rmd for dropkick and dropletqc
html 9eb9fcc cazodi 2022-03-01 add rmd for dropkick and dropletqc
Rmd a1fa048 cazodi 2022-03-01 fix cellbenderGPU and update lenti downstream analysis
html a1fa048 cazodi 2022-03-01 fix cellbenderGPU and update lenti downstream analysis
Rmd 0f7f43b cazodi 2022-02-28 lenti barcodes vs vireo results for ipscs
html 0f7f43b cazodi 2022-02-28 lenti barcodes vs vireo results for ipscs
Rmd bddd52c cazodi 2022-02-25 lenti barcode analysis
html bddd52c cazodi 2022-02-25 lenti barcode analysis
Rmd 8e5ef43 cazodi 2022-01-12 at2 analysis update
Rmd f75c7ba cazodi 2022-01-11 updated pipeline for pilot3
html f75c7ba cazodi 2022-01-11 updated pipeline for pilot3
Rmd 6a5fef0 cazodi 2021-10-01 posthoc dropletQC
html 6a5fef0 cazodi 2021-10-01 posthoc dropletQC
Rmd 1728604 cazodi 2021-09-29 add pilot1 analysis to workflowr
html 1728604 cazodi 2021-09-29 add pilot1 analysis to workflowr
Rmd 67135d3 cazodi 2021-09-28 added initial dropletQC results
html 67135d3 cazodi 2021-09-28 added initial dropletQC results
Rmd c703e21 cazodi 2021-09-27 added workflowr pages for cell calling with emptydroplet and dropkick
html c703e21 cazodi 2021-09-27 added workflowr pages for cell calling with emptydroplet and dropkick
Rmd e5d517e cazodi 2021-08-06 dropkick figures
html e5d517e cazodi 2021-08-06 dropkick figures
html 2899feb cazodi 2021-08-06 private to public
html 6f4a1f3 cazodi 2021-08-06 different link
Rmd 679ded7 cazodi 2021-08-06 updates for davis
html 679ded7 cazodi 2021-08-06 updates for davis
Rmd b200a1f cazodi 2020-03-18 removing accidental commits by christina…
Rmd 9057b09 cazodi 2020-03-18 Revert "initial repo change"
Rmd 0c6d3c6 cazodi 2020-03-18 initial repo change
Rmd c57ac08 Christina Azodi 2019-11-26 First init
Rmd b1f309c Davis McCarthy 2019-02-06 Updating template with improvements.
Rmd d73fd37 Davis McCarthy 2019-01-10 Initial commit

Project overview

Key findings:

Pilot #1

Complete report

Pilot #2

Data available 2021-04

  1. Cell calling
  2. Donor assignment
  3. Ambient RNA removal
  4. Final analysis 2022-04-22

A. HTO hashtag analysis

Pilot #3

Data available 2021-12-23

  1. Alignment & stats from cellRanger count:
  1. Stats from other cell calling tools:
  1. Called cell QC:
  1. Donor identification:

Side analyses:

  1. Lenti barcode analysis:

Pilot #4

Data available 2022-07-04


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