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Last updated: 2025-03-08

Checks: 2 0

Knit directory: duplex_sequencing_screen/

This reproducible R Markdown analysis was created with workflowr (version 1.6.2). The Checks tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.

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R Markdown file: up-to-date

Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.

Repository version: 836ad4b

Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility.

The results in this page were generated with repository version 836ad4b. See the Past versions tab to see a history of the changes made to the R Markdown and HTML files.

Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:

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Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.

---

These are the previous versions of the repository in which changes were made to the R Markdown (analysis/index.Rmd) and HTML (docs/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
Rmd	836ad4b	haiderinam	2025-03-08	Added tileseq error rates page
html	836ad4b	haiderinam	2025-03-08	Added tileseq error rates page
Rmd	cc571f5	haiderinam	2024-11-23	Added some Tileseq analyses
html	cc571f5	haiderinam	2024-11-23	Added some Tileseq analyses
Rmd	d28e862	haiderinam	2024-10-27	Updated variant caller to be able to process Tileseq samples
html	d28e862	haiderinam	2024-10-27	Updated variant caller to be able to process Tileseq samples
Rmd	5eba7e0	haiderinam	2024-10-14	Updated Github landing page
html	5eba7e0	haiderinam	2024-10-14	Updated Github landing page
Rmd	bac3c1e	haiderinam	2024-09-02	Updated the GitHub io landing page
html	bac3c1e	haiderinam	2024-09-02	Updated the GitHub io landing page
Rmd	667c6fb	haiderinam	2024-06-15	Analyses on gnomad-enabled ABL mutants
html	667c6fb	haiderinam	2024-06-15	Analyses on gnomad-enabled ABL mutants
Rmd	e57e36e	haiderinam	2024-04-29	Added ABL full kinase analyses
html	e57e36e	haiderinam	2024-04-29	Added ABL full kinase analyses
Rmd	268b0cf	haiderinam	2023-09-02	Added lane25a data (Shokat lab screens)
html	268b0cf	haiderinam	2023-09-02	Added lane25a data (Shokat lab screens)
Rmd	57fd1e7	haiderinam	2023-08-30	Updated various analyses and added to website
html	57fd1e7	haiderinam	2023-08-30	Updated various analyses and added to website
html	f9eea37	haiderinam	2023-08-30	2023 Updates
Rmd	8202ef7	haiderinam	2023-04-10	Added BE vs SM analyses on putative mutant
html	8202ef7	haiderinam	2023-04-10	Added BE vs SM analyses on putative mutant
Rmd	60b906b	haiderinam	2023-04-10	Added ROC analyses on BE-SM data
html	60b906b	haiderinam	2023-04-10	Added ROC analyses on BE-SM data
Rmd	a33eea5	haiderinam	2023-03-25	Added ABL CDF Analyses of evenness
html	a33eea5	haiderinam	2023-03-25	Added ABL CDF Analyses of evenness
Rmd	81a5af3	haiderinam	2023-02-25	Added shortest codon finder function
Rmd	fa7baf1	haiderinam	2022-12-15	Updates to the variant caller
html	fabfb30	haiderinam	2022-12-09	Build site.
Rmd	077edd0	haiderinam	2022-12-09	Added K562 Webpage
html	077edd0	haiderinam	2022-12-09	Added K562 Webpage
Rmd	cec2e31	haiderinam	2022-12-08	Added error rate analyses
html	cec2e31	haiderinam	2022-12-08	Added error rate analyses
html	404fc72	haiderinam	2022-11-04	Build site.
Rmd	ff4b4e8	haiderinam	2022-11-04	wflow_publish("analysis/index.Rmd")
Rmd	3a2f887	haiderinam	2022-11-04	Added analyses of IL3 independence
Rmd	6f54acf	haiderinam	2022-11-04	Added analyses of SSCS vs DCS error rates
html	28519e7	haiderinam	2022-10-29	Build site.
Rmd	ba25cb7	haiderinam	2022-10-29	wflow_publish("analysis/index.Rmd")
Rmd	7ed0af8	haiderinam	2022-08-22	August 2022 Updates
html	86ce8ca	haiderinam	2022-08-22	August 2022 Update
html	f368371	haiderinam	2020-08-13	Build site.
html	7fe0f9b	haiderinam	2020-07-06	Build site.
Rmd	e4a901d	haiderinam	2020-07-06	wflow_publish("analysis/index.Rmd")
html	231d21d	haiderinam	2020-06-07	Build site.
html	8f50f99	haiderinam	2020-06-07	Build site.
Rmd	5da3af0	haiderinam	2020-06-07	wflow_publish("analysis/index.Rmd")
html	75ddcb1	haiderinam	2020-06-02	Build site.
Rmd	a173683	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	bd2dec5	haiderinam	2020-06-02	Build site.
Rmd	1bb5940	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	c43acef	haiderinam	2020-06-02	Build site.
Rmd	d5c9f64	haiderinam	2020-06-02	wflow_publish("analysis/index.Rmd")
html	eaca616	haiderinam	2020-04-20	Build site.
Rmd	2bba93e	haiderinam	2020-04-20	wflow_publish("analysis/*.Rmd")
html	05e3df6	haiderinam	2020-04-07	Build site.
html	1c86f69	haiderinam	2020-04-07	Build site.
Rmd	e731909	haiderinam	2020-04-07	wflow_publish("analysis/index.Rmd")
html	4516a7f	haiderinam	2020-04-06	Build site.
Rmd	3a57291	haiderinam	2020-04-06	wflow_publish(files = "analysis/index.Rmd")
html	c2930d5	haiderinam	2020-04-03	Build site.
Rmd	52f6884	haiderinam	2020-04-03	wflow_publish("analysis/*.Rmd")
html	6af2cdc	haiderinam	2020-04-03	Build site.
Rmd	5cda9d3	haiderinam	2020-04-03	wflow_publish("analysis/*.Rmd")
html	0b9b87b	haiderinam	2020-04-02	Build site.
Rmd	fc5b9c0	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	2bce927	haiderinam	2020-04-02	Build site.
html	4ed9b35	haiderinam	2020-04-02	Build site.
Rmd	e31836a	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	99181d5	haiderinam	2020-04-02	Build site.
Rmd	17c01d4	haiderinam	2020-04-02	wflow_publish("analysis/index.Rmd")
html	1e2f469	haiderinam	2020-04-02	Build site.
html	e11eec5	haiderinam	2020-04-02	Build site.
Rmd	0053f96	haiderinam	2020-04-02	wflow_publish("analysis/*.Rmd")
html	b1cbbfa	haiderinam	2020-04-02	Build site.
Rmd	703346a	haiderinam	2020-04-02	Start workflowr project.

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BCR ABL Deep Mutational Scan

• Click here to analyses of the growth mutant standards under drug at low allele frequencies.
  

• Click here to view various computational improvements including: logistic regressions of dose-response curves, predicting the effect on fitness of dosing errors.
  

• Click here to view DMS analyses.
  

• Click here view analyses interpreting variants of uncertain drug resistance in ABL.
  

• Click here to view base editing analyses.
  

• Click here to view our validation IC50s with hits from the DMS screens.

• Click here to view our analyses on error rates in Tileseq vs NGS vs Duplex sequencing.
  

• Click here to view our analyses on the error rates in spike-in data when using LFCs vs Net growth rates.
  

Click here to be redirected to the github page that contains all the data and analysis rmd files.

What is in each directory:

• Data: contains data downloaded prior to analyses.
  
• Output: contains data that the code makes
  
• Analysis: contains your Rmarkdown files with the code.
  
• Docs: contain the html output from the Rmd files in the analysis directory.
  
• Code: contains .R files that are functions that the Rmd files in the analysis folder use.