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CHANGELOG.md

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Changelog

All notable changes to this project will be documented in this file.

Unrelease

[2.0] - 2021-05-27

  • Add modifications of bioinformatic Rouen teams

https://github.com/raphaelleman/SPiP/commit/9d8328fe15f4261b6684dcc69cd73beb818c2d57 https://github.com/raphaelleman/SPiP/commit/ad1f0e134e943ada2501ee165806d8245a41c589 https://github.com/raphaelleman/SPiP/commit/5e5bb35cc38bcc19f9b20465004781f63fbb5574 https://github.com/raphaelleman/SPiP/commit/9139871f06549470f724ca365d7394535b41f91a https://github.com/raphaelleman/SPiP/commit/4162f45b0c5c6e2a5ed7db4bdcb773f36523a6f5 https://github.com/raphaelleman/SPiP/commit/a846ce8f68ab4a475e71cc3a547f4aa34ded69f2 https://github.com/raphaelleman/SPiP/commit/c3d2241ebb898c1eb0b163262cc0ec9a9f61991c https://github.com/raphaelleman/SPiP/commit/9beafafee541caa175643e8f16d400873f2c3a5b https://github.com/raphaelleman/SPiP/commit/ad774fe05817e4a358125f087c65944eda39716d https://github.com/raphaelleman/SPiP/commit/1fd5bc783facdbe8d987f4e18b37f6c6e684ab5b https://github.com/raphaelleman/SPiP/commit/e6b6295da8a1452120d2e7af3014ebf5ed61fea3 https://github.com/raphaelleman/SPiP/commit/116412bb4c751d56568a3efb0b67db3b8552628e https://github.com/raphaelleman/SPiP/commit/1dc2f6d1719863534d8a16dfb2782805fa36fe11 https://github.com/raphaelleman/SPiP/commit/32ba2e000d78a0346a2577d6c991d2b6ae5e0123

[2.0] - 2021-03-08

  • Add random forest algorithm
  • change VPP/VPN tables

https://github.com/raphaelleman/SPiP/commit/dc0d3e81119924606e70480eb9e0671a9ecea311 https://github.com/raphaelleman/SPiP/commit/d784b1ce58d446f41457dea9f34aaac152dd1f94

1.1 - 2021-01-08

  • Use RData files instead of samtools to get sequences
  • Add two options to select gene or transcript to analyze
  • Redefine window to find potential cryptic splice sites

https://github.com/raphaelleman/SPiP/commit/da471b163a802f2707829e48a171c5b5a5e2bc50
https://github.com/raphaelleman/SPiP/commit/68e74eef7d935b52b62e5d65d852515f815dbdb0
https://github.com/raphaelleman/SPiP/commit/236c22eaa8d2f803c22518a247e09bb97591e699
https://github.com/raphaelleman/SPiP/commit/17b850ec175c07ff3a3c006f0a0e7b732d9c3113

[1.0] - 2020-05-15

  • Change the size of the window to scn for cryptic/de novo creation
  • Update getRefSeqDatabase.r script
  • Update splicing probabilities
  • Update output text of SPiP
  • Change VCF example file
  • Add policy to the SPiP script

https://github.com/raphaelleman/SPiP/commit/e3ce1878b4a8f1ea30e2ddab778fbe646f6f8cef
https://github.com/raphaelleman/SPiP/commit/9e677cb4776f24f08738a87e251f908c9ca4f1e8
https://github.com/raphaelleman/SPiP/commit/84b6510d10ac03f9a8bbbe8132766d1d2e2cc5de
https://github.com/raphaelleman/SPiP/commit/b17569d98c7446ad24531e2d34eef3c3f59bc9e0
https://github.com/raphaelleman/SPiP/commit/cf5b8b0b1a35e013d09b9075be80c1bee12c9b84
https://github.com/raphaelleman/SPiP/commit/573a4e42353aad0d4107d2fd8f75eb4379c60b7e
https://github.com/raphaelleman/SPiP/commit/e87fd77f2d4b3c2f3201b8f6393a4423c41aa8f5

[0.6.1] - 2020-04-24

  • Check if samtools is executalbe
  • Add function to read fa.fai file to get the chromosome nomenclature

https://github.com/raphaelleman/SPiP/commit/e1b9965742760db49cdf3680438b92927dc748ba

0.6 - 2020-03-06

  • Add exonic information
  • Add function to get output in VCF format
  • Change the parallel package to foreach and doParallel
  • Remove function to get sequence by web API
  • Add a MIT license
  • Add ASCII logo

https://github.com/raphaelleman/SPiP/commit/879568f540711b4c6e7f5f015708be6b4d645ef8
https://github.com/raphaelleman/SPiP/commit/dece37f570907412658cf929b4c0516ed9cac33f
https://github.com/raphaelleman/SPiP/commit/e756ad3662c8f5bde624b25661e2ea5c15d02e81
https://github.com/raphaelleman/SPiP/commit/c92b3664e368b3abe50bc55bd555d555277fc20f
https://github.com/raphaelleman/SPiP/commit/51230f9a2945f9952eebff0c5d8c507338c86b05
https://github.com/raphaelleman/SPiP/commit/03fb95b24249220dc58774d1633ab1b0c9517a68
https://github.com/raphaelleman/SPiP/commit/9dd9c034ed8ed539aac6347c302721043d847cfb
https://github.com/raphaelleman/SPiP/commit/293cdb290d77f4df0492bff987b0b84c03d73c73
https://github.com/raphaelleman/SPiP/commit/901a4e65e506a84646b29fa82f929457c66d8de9
https://github.com/raphaelleman/SPiP/commit/295d93c19e570d28bb87f81c6c2520374c9bd226

[0.5.1] - 2020-01-16

  • Corrected error from the convertion transcriptomic coordinates to genomic coordinates

https://github.com/raphaelleman/SPiP/commit/405e0c83aee735a56b9ca0192f387eebbf1ada51
https://github.com/raphaelleman/SPiP/commit/ae2d60d381bf4047a2c82c6e08579a712b017bb5
https://github.com/raphaelleman/SPiP/commit/ebeb5bba11dc08e3bb0689af16bdcddd38809ee4

0.5 - 2019-12-17

  • Update the output of SPiP + add gene names
  • Create a new logo
  • Update ESR threshold to -1.10

https://github.com/raphaelleman/SPiP/commit/71a8c45f6479deae87856ed4af89f38625ec2ab2
https://github.com/raphaelleman/SPiP/commit/548230ed44d2f293e6e40a5764dead2d87e82dd9
https://github.com/raphaelleman/SPiP/commit/3947bcc3a0892fc0a0f2ece445cf702959c43d7b
https://github.com/raphaelleman/SPiP/commit/f734cb05634f8b71a81897be403d91588676cd1e

[0.4.2] - 2019-09-27

  • Update probabilites of splicing alteration

https://github.com/raphaelleman/SPiP/commit/031ee967eb3bb0bc375adbc60fa11f2f21a1e9ca

[0.4.1] - 2019-07-23

  • Update VCF functions to take into account the meat-information of VCF files used as input

https://github.com/raphaelleman/SPiP/commit/688305a19251d8cb89687c6bf130f012831042d5

0.4 - 2019-07-01

  • Remove options to choice tools used by SPiP
  • Update the output of SPiP

https://github.com/raphaelleman/SPiP/commit/b8b7a69066dcc5b5c3e1e13294c8a038200fb784
https://github.com/raphaelleman/SPiP/commit/5a4fc118cb6a5d8cd1a601aae19490e9305b565c
https://github.com/raphaelleman/SPiP/commit/7969f71def1f9d8683bfa16a072d0a435e175e3d
https://github.com/raphaelleman/SPiP/commit/6853376703e38bbe891d55c48df7318d38623e4b

[0.3.1] - 2019-05-24

  • Corrected convertion transcriptomic coordinates to genomic coordinates

https://github.com/raphaelleman/SPiP/commit/ab615730064116888311a1da16f0dd120440faad

0.3 - 2019-05-16

  • Add meta-header to the output
  • Update probabilities of splicing
  • Add the flag 'de novo' for splice site creation
  • Add the PDF manual of SPiP
  • Corrected getRefSeqDatabase.r to add gene names

https://github.com/raphaelleman/SPiP/commit/559ba236c773209019e5d8ce2eef0d18c3efdd79
https://github.com/raphaelleman/SPiP/commit/702984e32be464fc58b51201c68d979c9f8b7927
https://github.com/raphaelleman/SPiP/commit/e4d988fac1f939e69cb9218c72e048bc96c172b2

[0.2.4] - 2019-05-07

  • Add getRefSeqDatabase.r srcipt permitting to reload and adapte RefSaq database for SPiP
  • Add checking function to known if the DNA sequence permits to calculate scores
  • Change the README file
  • Add VCF file as an example from 1000 Genomes data

https://github.com/raphaelleman/SPiP/commit/f9bfb6513165a7fba8e36b47c38fc307ad9c7202
https://github.com/raphaelleman/SPiP/commit/c913f0aa775d2070248c9bf5834f3d6ad266eca9
https://github.com/raphaelleman/SPiP/commit/96a0ea5cf7d33161c8b4c7a1e731d4363298e485
https://github.com/raphaelleman/SPiP/commit/b37529138f8d9dcef905ff741bb8905f81fec467
https://github.com/raphaelleman/SPiP/commit/c76fc6d369f7670c137353c1a5e98b0b7930d79a
https://github.com/raphaelleman/SPiP/commit/3276a621afd4ff06bd52909a7067aa9e1b5aae83

[0.2.3] - 2019-04-29

  • Corrected VCF reading functions

https://github.com/raphaelleman/SPiP/commit/749d13742157b3f3c4c8abc43f0d201342a291d1

[0.2.2] - 2019-04-04

  • Corrected parallel functions

https://github.com/raphaelleman/SPiP/commit/fabfd133fb70ba6513221b2752e5a6b49654d2f2

[0.2.1] - 2019-03-28

  • Add parallel options

https://github.com/raphaelleman/SPiP/commit/bd19031d2ed2dab160177aea41bf6ea76f3c2176

0.2 - 2019-03-01

https://github.com/raphaelleman/SPiP/commit/ad5bdcb94e5a798dc5f80ba9fcc46187e1418ab1
https://github.com/raphaelleman/SPiP/commit/0c681edc71ae85eaacb0771c1bd14bd11753bdb6
https://github.com/raphaelleman/SPiP/commit/98c7198959e66e47bb629040175842810144f015
https://github.com/raphaelleman/SPiP/commit/7f9d821588ec1ab3403683f9d6b6fcbe599243b3
https://github.com/raphaelleman/SPiP/commit/39e6aa5b9d9958adb52821c60494c93c533e3541
https://github.com/raphaelleman/SPiP/commit/4e9d2aa09ff4500cd693b9e699432afdc1021e38

0.1 - 2019-02-19

  • First version online only for Windows OS