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Run de seq 1 0 #28

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wants to merge 66 commits into from
Closed

Run de seq 1 0 #28

wants to merge 66 commits into from

Commits on Jun 22, 2021

  1. Adding script to run DESeq analysis

    @sangeetashukla
    sangeetashukla committed Jun 22, 2021
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  2. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jun 22, 2021
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Commits on Jun 24, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jun 24, 2021
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Commits on Jul 15, 2021

  1. Committing updated module

    @sangeetashukla
    sangeetashukla committed Jul 15, 2021
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  2. Committing updated Uberon codes

    @sangeetashukla
    sangeetashukla committed Jul 15, 2021
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  3. Merge branch 'run-DESeq-1-0' of https://github.com/sangeetashukla/Ope… 

    …nPedCan-analysis into run-DESeq-1-0
    @sangeetashukla
    sangeetashukla committed Jul 15, 2021
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  4. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jul 15, 2021
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Commits on Jul 16, 2021

  1. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  2. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  3. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  4. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  5. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  6. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  7. Update analyses/DESeq_analysis/run-DESeq-analysis.R 

    Co-authored-by: Yuanchao Zhang <logstar@users.noreply.github.com>
    @sangeetashukla @logstar
    sangeetashukla and logstar authored Jul 16, 2021
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  8. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jul 16, 2021
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Commits on Jul 20, 2021

  1. Fixed the data file paths to run from the .\analyses. Fixed the varia… 

    …ble assignments to use '<-' istead of '='
    @sangeetashukla
    sangeetashukla committed Jul 20, 2021
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  2. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jul 20, 2021
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  3. Merge branch 'run-DESeq-1-0' of https://github.com/sangeetashukla/Ope… 

    …nPedCan-analysis into run-DESeq-1-0
    @sangeetashukla
    sangeetashukla committed Jul 20, 2021
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Commits on Jul 22, 2021

  1. Fixed a few typos. Will edit the script later again to fix the path f… 

    …or the data files
    @sangeetashukla
    sangeetashukla committed Jul 22, 2021
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Commits on Jul 28, 2021

  1. Edited R script to accept data files as command line arguments, added… 

    … a sample Results file, and included Dockerfile that works with this module
    @sangeetashukla
    sangeetashukla committed Jul 28, 2021
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  2. Update run-DESeq-analysis.R

    @sangeetashukla
    sangeetashukla authored Jul 28, 2021
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  3. Added a line to install an R package

    @sangeetashukla
    sangeetashukla committed Jul 28, 2021
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  4. Added a line to install an R package

    @sangeetashukla
    sangeetashukla committed Jul 28, 2021
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  5. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Jul 28, 2021
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Commits on Aug 2, 2021

  1. Edit dockerfile to include call to shell script

    @sangeetashukla
    sangeetashukla committed Aug 2, 2021
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  2. Edited file to work with a shell script for call and input files, fix… 

    …ed a few bugs described in the PR
    @sangeetashukla
    sangeetashukla committed Aug 2, 2021
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  3. Adding shell script to call the R script and pass input files

    @sangeetashukla
    sangeetashukla committed Aug 2, 2021
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  4. Merge branch 'run-DESeq-1-0' of https://github.com/sangeetashukla/Ope… 

    …nPedCan-analysis into run-DESeq-1-0
    @sangeetashukla
    sangeetashukla committed Aug 2, 2021
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  5. Updated to fix a bug

    @sangeetashukla
    sangeetashukla committed Aug 2, 2021
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Commits on Aug 3, 2021

  1. adding script to transform json files to a single jsonl file

    @sangeetashukla
    sangeetashukla committed Aug 3, 2021
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Commits on Aug 4, 2021

  1. Adding script to transform JSON to JSON L. Edited R script to include… 

    … lines to create JSON tables
    @sangeetashukla
    sangeetashukla committed Aug 4, 2021
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Commits on Aug 6, 2021

  1. Update run-DESeq-analysis.R 

    Previous git push did not push all local changes. This is to include all changes described in the previous commit/push.
    @sangeetashukla
    sangeetashukla authored Aug 6, 2021
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Commits on Aug 10, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Aug 10, 2021
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  2. included UBERON codes in output

    @sangeetashukla
    sangeetashukla authored Aug 10, 2021
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  3. Adding sample result files from sample data for testing

    @sangeetashukla
    sangeetashukla authored Aug 10, 2021
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  4. Remote typos/comments in run_deseq.sh

    @sangeetashukla
    sangeetashukla authored Aug 10, 2021
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Commits on Aug 11, 2021

  1. Adding scripts to create data for testing of module

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  2. Adding compressed test data and sample results from that test data pr… 

    …ocessing
    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  3. Changed a script name and removed typos

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  4. Syncing files with intuitive names

    @sangeetashukla
    sangeetashukla committed Aug 11, 2021
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  5. Adding README

    @sangeetashukla
    sangeetashukla committed Aug 11, 2021
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  6. Moved the contents to a new script

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  7. Moved contents to a new script

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  8. Removing since the main script will create jsonl files

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  9. Updated README

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  10. Edited file name in the description

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  11. Edited a column name for the final data table.

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  12. Not required anymore

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  13. Not needed anymore

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  14. Removing to replace with a new file

    @sangeetashukla
    sangeetashukla authored Aug 11, 2021
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  15. Dockerfile for CAVATICA app

    @sangeetashukla
    sangeetashukla committed Aug 11, 2021
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Commits on Aug 23, 2021

  1. Adding compressed jsonl file for all comparisons as run on HPC

    @sangeetashukla
    sangeetashukla committed Aug 23, 2021
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  2. Script to calculate HIST_index, GTEx_Index, and subset histology and … 

    …counts data
    @sangeetashukla
    sangeetashukla committed Aug 23, 2021
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  3. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Aug 23, 2021
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  4. Edited - Takes input files from Input-Subsetting

    @sangeetashukla
    sangeetashukla authored Aug 23, 2021
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Commits on Aug 24, 2021

  1. Updated Dockerfile for Cavatica

    @sangeetashukla
    sangeetashukla authored Aug 24, 2021
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  2. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Aug 24, 2021
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  3. Edited to only include R scripts and required R packages

    @sangeetashukla
    sangeetashukla authored Aug 24, 2021
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  4. Updated for compatibility with Dockerfile for Cavatica

    @sangeetashukla
    sangeetashukla authored Aug 24, 2021
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  5. Updated for compatibility with Dockerfile for Cavatica

    @sangeetashukla
    sangeetashukla authored Aug 24, 2021
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Commits on Sep 1, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Sep 1, 2021
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Commits on Sep 2, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Sep 2, 2021
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Commits on Sep 8, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Sep 8, 2021
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  2. Updated to change threshold of sample size to run DESeq per cancer_group

    @sangeetashukla
    sangeetashukla authored Sep 8, 2021
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  3. Updated threshold for sample size to run DESeq analysis per cancer_group

    @sangeetashukla
    sangeetashukla authored Sep 8, 2021
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Commits on Sep 13, 2021

  1. Merge branch 'PediatricOpenTargets:dev' into run-DESeq-1-0

    @sangeetashukla
    sangeetashukla authored Sep 13, 2021
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