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copy august 2024 course
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‎.gitignore‎

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.DS_Store
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.idea/*
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_site/*

‎Annotation_file_timsTOF.txt‎

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File name Patient ID Pseudonym Sample ID Diagnosis from tumorbank Gender IGHV.status trisomy12 DDX3X NOTCH1 SF3B1 del11q Leukocyte count treatStatus
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fmeierab_T190525_CLL_diaPASEF_01_1976.d P0002 M76U 12PB0459 CLL m M 0 1 135000 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_02_1977.d P0004 JQ6C 12PB0071 CLL m M 1 51900 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_03_1978.d P0018 PQR8 12PB0088 CLL f U 0 74490 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_04_1979.d P0021 M7OV 13PB0657 CLL m M 1 193600 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_05_1980.d P0024 FSHB 12PB0274 CLL f M 0 36720 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_06_1981.d P0027 OVF5 15PB0026 CLL m M 0 1 41330 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_07_1982.d P0029 Q145 11PB0056 CLL m M 0 78710 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_08_1983.d P0036 YNIY 12PB0110 CLL m U 0 224300 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_09_1984.d P0038 FBE8 11PB0359 CLL f M 1 206100 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_10_1985.d P0043 9S37 12PB0190 CLL m U 0 56850 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_11_1986.d P0045 15W9 11PB0055 CLL f M 1 45640 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_12_1987.d P0047 CI7B 14PB0535 CLL f M 0 1 81360 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_13_1988.d P0053 1A5K 15PB0154 CLL m M 0 62110 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_14_1989.d P0069 8E7F 14PB0002 CLL m U 0 1 25130 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_15_1990.d P0087 ZRWN 13PB0003 CLL f U 1 82690 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_16_1991.d P0094 SUEK 12PB0019 CLL f M 0 137100 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_17_1992.d P0098 Y0AO 15PB0089 CLL m M 1 99480 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_18_1993.d P0100 3DMC 13PB0145 CLL m M 0 56550 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_19_2003.d P0105 ECD1 13PB0576 CLL f M 0 1 1 161100 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_20_2004.d P0107 7RHI 13PB0107 CLL m M 1 81690 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_21_2005.d P0108 PK0F 13PB0014 CLL m U 0 69680 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_22_2006.d P0293 P4GM 11PB0371 CLL m U 0 1 24100 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_23_2007.d P0345 0M1Z 14PB0075 CLL f M 1 33370 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_24_2008.d P0352 TMVO 12PB0117 CLL m U 0 1 1 30930 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_25_1950.d P0356 TSYU 12PB0139 CLL m U 1 40890 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_26_1951.d P0359 HP01 14PB0218 CLL m U 0 56420 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_27_1952.d P0474 O1OE 13PB0559 CLL f U 1 1 76210 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_28_1953.d P0484 AJYE 13PB0051 CLL m U 0 1 186300 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_29_1954.d P0487 0XXE 12PB0499 CLL m U 1 1 36850 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_30_1955.d P0494 9ELC 13PB0522 CLL m M 1 103200 NA
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fmeierab_T190525_CLL_diaPASEF_31_1956.d P0518 QAG4 13PB0242 CLL m M 0 1 44140 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_32_1957.d P0538 9MI3 13PB0127 CLL m U 0 1 413000 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_33_1958.d P0581 K49C 13PB0228 CLL f U 0 65410 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_34_1959.d P0611 CLZEPV 13PB0291 CLL m M 1 23290 NA
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fmeierab_T190525_CLL_diaPASEF_35_1960.d P0615 SM9W 14PB0006 CLL f M 1 63590 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_36_1961.d P0641 P3S9 13PB0403 CLL m U 0 117300 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_37_1962.d P0648 72RM 13PB0420 CLL m M 1 1 43610 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_38_1963.d P0679 UAYJ 13PB0593 CLL f M 0 57310 NA
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fmeierab_T190525_CLL_diaPASEF_39_1964.d P0711 PFDT 13PB0571 CLL m U 1 1 99550 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_40_1965.d P0721 JLK0 14PB0398 CLL f U 1 22800 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_41_1966.d P0734 0UBS 14PB0021 CLL m U 0 1 106100 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_42_1967.d P0735 PFR1 13PB0653 CLL f M 1 89090 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_43_1968.d P0747 EMYM 14PB0050 CLL m U 0 1 124800 NA
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fmeierab_T190525_CLL_diaPASEF_44_1969.d P0781 3XLHSB 15PB0182 CLL f U 1 1 59070 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_45_1970.d P0818 MTGWKA 14PB0251 CLL m M 0 41460 NA
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fmeierab_T190525_CLL_diaPASEF_46_1971.d P0880 P1WSWP 14PB0298 CLL f U 1 1 217900 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_47_1972.d P0888 3U3F4R 14PB0326 CLL m U 1 1 134300 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_48_1973.d P0894 PURLLS 15PB0130 CLL m U 1 33230 beforeFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_49_1974.d P1005 QZNEKD 15PB0104 CLL m U 1 1 54480 afterFirstTreatment
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fmeierab_T190525_CLL_diaPASEF_50_1975.d P1075 L8HC49 16PB0056 CLL m U 0 1 1 0 1 30540 beforeFirstTreatment
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‎Gemfile‎

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source 'https://rubygems.org'
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gem 'github-pages', group: :jekyll_plugins

‎Gemfile.lock‎

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PLATFORMS
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ruby
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DEPENDENCIES
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github-pages
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BUNDLED WITH
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2.0.2

‎LICENSE‎

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BSD 3-Clause License
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Copyright (c) 2018, Kutay B. Sezginel
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All rights reserved.
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Redistribution and use in source and binary forms, with or without
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modification, are permitted provided that the following conditions are met:
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* Redistributions of source code must retain the above copyright notice, this
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list of conditions and the following disclaimer.
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* Redistributions in binary form must reproduce the above copyright notice,
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this list of conditions and the following disclaimer in the documentation
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and/or other materials provided with the distribution.
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* Neither the name of the copyright holder nor the names of its
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contributors may be used to endorse or promote products derived from
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this software without specific prior written permission.
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THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

‎README.md‎

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## Brief tutorial on limma for proteomics at the UC Davis Proteomics Short Course
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Documentation for this tutorial is at
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# https://ucdavis-bioinformatics-training.github.io/limma-proteomics-August-2024/

‎_config.yml‎

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theme: jekyll-theme-minimal
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title: 'Proteomics Analysis with Limma'
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show_downloads: True
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google_analytics: True
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navigation:
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- title: Home
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url: /
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- title: Setup
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url: setup
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- title: Analysis in limma
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url: limma_proteomics_tutorial_2024

‎index.md‎

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---
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layout: default
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---
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{% include_relative README.md %}

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