Code

Add SV/CN plotting and merge dev_cn#4

Code

Merged

soymintc merged 42 commits intoshahcompbio:mastershahcompbio/wgs_analysis:masterfrom soymintc:mastersoymintc/wgs_analysis:masterCopy head branch name to clipboardJul 21, 2023

+2,261-54

Commits

Commits on Mar 16, 2023

• add CN data class with plot function for selected cohorts and genes

  soymintc

  committed
  9f514a9

Commits on Mar 20, 2023

• add CN data class with plot function for selected cohorts and genes

  soymintc

  committed
  012b62d

• fix script so only fn and class imports are enabled

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  committed
  63ce5f8

• fix plot title n count

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  0694cd2

• add per-chromosome plot function to main class

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  f4fcd8f

• add readme

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  6e3071f

• fix readme to remove

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  committed
  89fce5d

• fix readme

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  a0c4614

• fix signature enumeration bug

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  aeeba92

• add results

  soymintc

  committed
  a9829db

• fix script name for import purposes, fix p-arm patching bug

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  29a6ce0

• fix readme to cope for import changes

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  0bd4c73

• fix results after p-arm color fix

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  542595e

• allow SPECTRUM-DLP input

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  committed
  57cfbc4

• add SPECTRUM-DLP plots

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  committed
  c26e016

• fix typo for beartype

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  b1b0ce0

• add SPECTRUM-DLP to readme

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  committed
  8153a21

• add SPECTRUM-DLP to readme

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  committed
  dfd144e

Commits on Mar 23, 2023

• add CN peak/trough detection

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  committed
  8564542

Commits on Apr 6, 2023

• add loading/saving files functionality

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  866efb4

• Merge branch 'dev_cn' of github.com:shahcompbio/wgs_analysis into dev_cn

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  committed
  ebde8c3

Commits on May 19, 2023

• fix cn_utils to add peak detection

  soymintc

  committed
  296a924

Commits on Jul 3, 2023

• run with SPECTRUM and Metacohort

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  committed
  27c9e84

Commits on Jul 12, 2023

• add cn and sv plotting functions

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  committed
  9acb3f9

Commits on Jul 13, 2023

• fix sv plotting for generalizatino

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  committed
  10f93ec

• add vcf and consensus csv parsing functionality

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  committed
  7e01cd8

Commits on Jul 14, 2023

• add ideogram

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  committed
  8f55b32

Commits on Jul 17, 2023

• add ideogram and cn plots

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  committed
  2d57e78

Commits on Jul 18, 2023

• fix semantic error for nonexisting genome version

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  committed
  fdce561

• fix cytobands fn return error

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  committed
  2a11014

• fix cytobands dataframe bug

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  8476e37

• add examples

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  e00adeb

• add read_table dtype

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  ee4697e

• fix gitignore

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  49a2c26

• fix example

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  committed
  00ccf56

• fix debug lines

  soymintc

  committed
  430eddb

• fix example

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  committed
  50d1d3a

Commits on Jul 19, 2023

• run after adding NOTCH3

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  committed
  93216f6

Commits on Jul 20, 2023

• add gene plotting

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  committed
  7f7ad74

• fix gene plot bugs

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  committed
  e5f4b8f

• fix function help

  soymintc

  committed
  147ad6b

Commits on Jul 21, 2023

• merge dev_cn

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  committed
  e3209f3