Files in matdoering/openPrimeR
Multiplex PCR Primer Design and Analysis

.Rbuildignore
.travis.yml
DESCRIPTION
NAMESPACE
R/AnalysisStats.R R/Comparison.R R/Data.R R/IO.R R/IO_view.R R/Input.R R/Ippolito.R R/Output.R R/Plots.R R/PrimerDesign.R R/PrimerEvaluation.R R/RefCoverage.R R/Scoring.R R/SettingsDoc.R R/TemplatesDoc.R R/Tiller.R R/ambiguity.R R/check_stop_codons.R R/con_annealing_temperature.R R/con_dimerization.R R/con_gc_clamp.R R/con_gc_ratio.R R/con_melting_temperature.R R/con_primer_coverage.R R/con_primer_efficiency.R R/con_primer_secondary_structures.R R/con_repeats.R R/con_runs.R R/con_template_secondary_structures.R R/constraints.R R/constraints_eval.R R/errors.R R/filters.R R/helper_functions.R R/initialize_primers.R R/initialize_primers_tree.R R/openPrimeR.R R/optimization_ILP.R R/optimization_algo.R R/optimization_global.R R/optimization_greedy.R R/plots_comparison.R R/plots_constraints.R R/plots_coverage.R R/plots_filtering.R R/primer_significance.R R/primers.R R/settings.R R/startApp.R
R/sysdata.rda
R/templates.R R/zzz.R README.md data-raw/Comparison.R
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000016_Marks1991.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000025_Glas1999.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000032_Persson1991.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000046_Cardona1995.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000067_vanEs1991.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000069_Rubinstein1998.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000081_vanEs1991_CDR.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000089_Chong2002.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000090_Weng1992.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000095_Glamann1998.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000098_Manheimer1991.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000099_Verhagen2000.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000157_Szczepa2001.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000200_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000201_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000203_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGHV/IPS000221_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000022_Marks1991.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000038_Persson1991.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000043_Cardona1995.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000045_Atkinson1996.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000049_Chen1986.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000062_Chen1987.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000063_Giachino1995.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000072_vanEs1991.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000078_Glamann1998.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000085_Manheimer1991.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000088_Rubinstein1998.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000093_vanBurg2001.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000115_Pongers1999.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000121_Cox1994.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000122_Padyukov2001.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000126_Padyukov2001.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000154_Juul1997.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000158_Huber1993.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000160_Timmers1993.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000164_Beishuizen1997.fasta
data-raw/IMGT_data/IMGT_primers/IGKV/IPS000206_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/.Tiller2008_IGLV_1st.txt.swp
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000024_Marks1991.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000066_Cardona1995.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000073_Stiernholm1994.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000083_Moraes2003.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000114_vanBurg2001.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000145_Rubinstein1998.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000208_vanDongen2003.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000240_Farner1999_1st.fasta
data-raw/IMGT_data/IMGT_primers/IGLV/IPS000241-251_Farner1999_2nd.fasta
data-raw/IMGT_data/literature_primers/IGHV/Brezinschek1995_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Brezinschek1995_IGHV_2nd.fasta
data-raw/IMGT_data/literature_primers/IGHV/Ippolito2012_IGHV.fasta
data-raw/IMGT_data/literature_primers/IGHV/Kueppers1993_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Lim2010_IGHV.fasta
data-raw/IMGT_data/literature_primers/IGHV/Murugan2015_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Murugan2015_IGHV_2nd.fasta
data-raw/IMGT_data/literature_primers/IGHV/Sblattero1998_IGHV.fasta
data-raw/IMGT_data/literature_primers/IGHV/Scheid2011_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Tiller2008_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Tiller2008_IGHV_2nd.fasta
data-raw/IMGT_data/literature_primers/IGHV/Wardemann2003_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGHV/Wu2010_IGHV_1st.fasta
data-raw/IMGT_data/literature_primers/IGKV/Ippolito2014_IGKV.fasta
data-raw/IMGT_data/literature_primers/IGKV/Kueppers1993_IGKV_1st.fasta
data-raw/IMGT_data/literature_primers/IGKV/Lim2010_IGKV.fasta
data-raw/IMGT_data/literature_primers/IGKV/Murugan2015_IGKV_1st.fasta
data-raw/IMGT_data/literature_primers/IGKV/Murugan2015_IGKV_2nd.fasta
data-raw/IMGT_data/literature_primers/IGKV/Sblattero1998_IGKV.fasta
data-raw/IMGT_data/literature_primers/IGKV/Tiller2008_IGKV_1st.fasta
data-raw/IMGT_data/literature_primers/IGKV/Wardemann2003_IGKV_1st.fasta
data-raw/IMGT_data/literature_primers/IGLV/Ippolito2014_IGLV.fasta
data-raw/IMGT_data/literature_primers/IGLV/Lim2010_IGLV.fasta
data-raw/IMGT_data/literature_primers/IGLV/Murugan2015_IGLV_1nd.fasta
data-raw/IMGT_data/literature_primers/IGLV/Murugan2015_IGLV_1st.fasta
data-raw/IMGT_data/literature_primers/IGLV/Sblattero1998_IGLV.fasta
data-raw/IMGT_data/literature_primers/IGLV/Tiller2008_IGLV_1st.fasta
data-raw/IMGT_data/literature_primers/IGLV/Wardemann2003_IGLV_1st.fasta
data-raw/IMGT_data/primers/IGHV/Brezinschek1995_1st.fasta
data-raw/IMGT_data/primers/IGHV/Brezinschek1995_2nd.fasta
data-raw/IMGT_data/primers/IGHV/Cardona1995.fasta
data-raw/IMGT_data/primers/IGHV/Chong2002.fasta
data-raw/IMGT_data/primers/IGHV/Glamann1998.fasta
data-raw/IMGT_data/primers/IGHV/Glas1999.fasta
data-raw/IMGT_data/primers/IGHV/Ippolito2012.fasta
data-raw/IMGT_data/primers/IGHV/Kueppers1993.fasta
data-raw/IMGT_data/primers/IGHV/Lim2010.fasta
data-raw/IMGT_data/primers/IGHV/Manheimer1991.fasta
data-raw/IMGT_data/primers/IGHV/Marks1991.fasta
data-raw/IMGT_data/primers/IGHV/Murugan2015_1st.fasta
data-raw/IMGT_data/primers/IGHV/Murugan2015_2nd.fasta
data-raw/IMGT_data/primers/IGHV/Persson1991.fasta
data-raw/IMGT_data/primers/IGHV/Rubinstein1998.fasta
data-raw/IMGT_data/primers/IGHV/Sblattero1998.fasta
data-raw/IMGT_data/primers/IGHV/Scheid2011.fasta
data-raw/IMGT_data/primers/IGHV/Szczepa2001.fasta
data-raw/IMGT_data/primers/IGHV/Tiller2008_1st.fasta
data-raw/IMGT_data/primers/IGHV/Tiller2008_2nd.fasta
data-raw/IMGT_data/primers/IGHV/Verhagen2000.fasta
data-raw/IMGT_data/primers/IGHV/Wardemann2003.fasta
data-raw/IMGT_data/primers/IGHV/Weng1992.fasta
data-raw/IMGT_data/primers/IGHV/Wu2010.fasta
data-raw/IMGT_data/primers/IGHV/openPrimeR2017.fasta
data-raw/IMGT_data/primers/IGHV/vanDongen2003_A.fasta
data-raw/IMGT_data/primers/IGHV/vanDongen2003_B.fasta
data-raw/IMGT_data/primers/IGHV/vanDongen2003_C.fasta
data-raw/IMGT_data/primers/IGHV/vanDongen2003_single.fasta
data-raw/IMGT_data/primers/IGHV/vanEs1991.fasta
data-raw/IMGT_data/primers/IGHV/vanEs1991_CDR.fasta
data-raw/IMGT_data/primers/IGKV/Atkinson1996.fasta
data-raw/IMGT_data/primers/IGKV/Beishuizen1997.fasta
data-raw/IMGT_data/primers/IGKV/Cardona1995.fasta
data-raw/IMGT_data/primers/IGKV/Chen1986.fasta
data-raw/IMGT_data/primers/IGKV/Chen1987.fasta
data-raw/IMGT_data/primers/IGKV/Cox1994.fasta
data-raw/IMGT_data/primers/IGKV/Giachino1995.fasta
data-raw/IMGT_data/primers/IGKV/Glamann1998.fasta
data-raw/IMGT_data/primers/IGKV/Huber1993.fasta
data-raw/IMGT_data/primers/IGKV/Ippolito2012.fasta
data-raw/IMGT_data/primers/IGKV/Juul1997.fasta
data-raw/IMGT_data/primers/IGKV/Kueppers1993.fasta
data-raw/IMGT_data/primers/IGKV/Lim2010.fasta
data-raw/IMGT_data/primers/IGKV/Manheimer1991.fasta
data-raw/IMGT_data/primers/IGKV/Marks1991.fasta
data-raw/IMGT_data/primers/IGKV/Murugan2015_1st.fasta
data-raw/IMGT_data/primers/IGKV/Murugan2015_2nd.fasta
data-raw/IMGT_data/primers/IGKV/Padyukov2001.fasta
data-raw/IMGT_data/primers/IGKV/Persson1991.fasta
data-raw/IMGT_data/primers/IGKV/Pongers1999.fasta
data-raw/IMGT_data/primers/IGKV/Rubinstein1998.fasta
data-raw/IMGT_data/primers/IGKV/Sblattero1998.fasta
data-raw/IMGT_data/primers/IGKV/Tiller2008.fasta
data-raw/IMGT_data/primers/IGKV/Timmers1993.fasta
data-raw/IMGT_data/primers/IGKV/Wardemann2003.fasta
data-raw/IMGT_data/primers/IGKV/openPrimeR2017.fasta
data-raw/IMGT_data/primers/IGKV/vanBurg2001.fasta
data-raw/IMGT_data/primers/IGKV/vanDongen2003.fasta
data-raw/IMGT_data/primers/IGKV/vanEs1991.fasta
data-raw/IMGT_data/primers/IGLV/Cardona1995.fasta
data-raw/IMGT_data/primers/IGLV/Farner1999_1st.fasta
data-raw/IMGT_data/primers/IGLV/Farner1999_2nd.fasta
data-raw/IMGT_data/primers/IGLV/Ippolito2012.fasta
data-raw/IMGT_data/primers/IGLV/Lim2010.fasta
data-raw/IMGT_data/primers/IGLV/Marks1991.fasta
data-raw/IMGT_data/primers/IGLV/Moraes2003.fasta
data-raw/IMGT_data/primers/IGLV/Murugan2015_1st.fasta
data-raw/IMGT_data/primers/IGLV/Murugan2015_2nd.fasta
data-raw/IMGT_data/primers/IGLV/Rubinstein1998.fasta
data-raw/IMGT_data/primers/IGLV/Sblattero1998.fasta
data-raw/IMGT_data/primers/IGLV/Stiernholm1994.fasta
data-raw/IMGT_data/primers/IGLV/Tiller2008.fasta
data-raw/IMGT_data/primers/IGLV/Wardemann2003.fasta
data-raw/IMGT_data/primers/IGLV/openPrimeR2017.fasta
data-raw/IMGT_data/primers/IGLV/vanBurg2001.fasta
data-raw/IMGT_data/primers/IGLV/vanDongen2003.fasta
data-raw/IMGT_data/primers_mod/IGH/Glamann1998.fasta
data-raw/IMGT_data/primers_mod/IGH/Kueppers1993.fasta
data-raw/IMGT_data/primers_mod/IGH/Persson1991.fasta
data-raw/IMGT_data/primers_mod/IGH/Rubinstein1998.fasta
data-raw/IMGT_data/primers_mod/IGH/vanEs1991.fasta
data-raw/IMGT_data/primers_mod/IGK/Atkinson1996.fasta
data-raw/IMGT_data/primers_mod/IGK/Cox1994.fasta
data-raw/IMGT_data/primers_mod/IGK/Glamann1998.fasta
data-raw/IMGT_data/primers_mod/IGK/Juul1997.fasta
data-raw/IMGT_data/primers_mod/IGK/Kueppers1993.fasta
data-raw/IMGT_data/primers_mod/IGK/Padyukov2001.fasta
data-raw/IMGT_data/primers_mod/IGK/Persson1991.fasta
data-raw/IMGT_data/primers_mod/IGK/Rubinstein1998.fasta
data-raw/IMGT_data/primers_mod/IGK/Timmers1993.fasta
data-raw/IMGT_data/primers_mod/IGL/Moraes2003.fasta
data-raw/IMGT_data/primers_mod/IGL/Rubinstein1998.fasta
data-raw/IMGT_data/primers_mod/adaptor_info.txt
data-raw/IMGT_data/primers_raw/IGHV/Brezinschek1995_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Brezinschek1995_IGHV_2nd.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000016_Marks1991.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000025_Glas1999.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000032_Persson1991.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000046_Cardona1995.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000067_vanEs1991.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000069_Rubinstein1998.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000081_vanEs1991_CDR.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000089_Chong2002.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000090_Weng1992.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000095_Glamann1998.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000098_Manheimer1991.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000099_Verhagen2000.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000157_Szczepa2001.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000200_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000201_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000203_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGHV/IPS000221_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGHV/Ippolito2012_IGHV.fasta
data-raw/IMGT_data/primers_raw/IGHV/Kueppers1993_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Lim2010_IGHV.fasta
data-raw/IMGT_data/primers_raw/IGHV/Murugan2015_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Murugan2015_IGHV_2nd.fasta
data-raw/IMGT_data/primers_raw/IGHV/Sblattero1998_IGHV.fasta
data-raw/IMGT_data/primers_raw/IGHV/Scheid2011_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Tiller2008_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Tiller2008_IGHV_2nd.fasta
data-raw/IMGT_data/primers_raw/IGHV/Wardemann2003_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGHV/Wu2010_IGHV_1st.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000022_Marks1991.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000038_Persson1991.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000043_Cardona1995.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000045_Atkinson1996.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000049_Chen1986.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000062_Chen1987.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000063_Giachino1995.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000072_vanEs1991.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000078_Glamann1998.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000085_Manheimer1991.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000088_Rubinstein1998.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000093_vanBurg2001.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000115_Pongers1999.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000121_Cox1994.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000122_Padyukov2001.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000126_Padyukov2001.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000154_Juul1997.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000158_Huber1993.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000160_Timmers1993.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000164_Beishuizen1997.fasta
data-raw/IMGT_data/primers_raw/IGKV/IPS000206_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGKV/Ippolito2014_IGKV.fasta
data-raw/IMGT_data/primers_raw/IGKV/Kueppers1993_IGKV_1st.fasta
data-raw/IMGT_data/primers_raw/IGKV/Lim2010_IGKV.fasta
data-raw/IMGT_data/primers_raw/IGKV/Murugan2015_IGKV_1st.fasta
data-raw/IMGT_data/primers_raw/IGKV/Murugan2015_IGKV_2nd.fasta
data-raw/IMGT_data/primers_raw/IGKV/Sblattero1998_IGKV.fasta
data-raw/IMGT_data/primers_raw/IGKV/Tiller2008_IGKV_1st.fasta
data-raw/IMGT_data/primers_raw/IGKV/Wardemann2003_IGKV_1st.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000024_Marks1991.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000066_Cardona1995.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000073_Stiernholm1994.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000083_Moraes2003.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000114_vanBurg2001.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000145_Rubinstein1998.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000208_vanDongen2003.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000240_Farner1999_1st.fasta
data-raw/IMGT_data/primers_raw/IGLV/IPS000241-251_Farner1999_2nd.fasta
data-raw/IMGT_data/primers_raw/IGLV/Ippolito2014_IGLV.fasta
data-raw/IMGT_data/primers_raw/IGLV/Lim2010_IGLV.fasta
data-raw/IMGT_data/primers_raw/IGLV/Murugan2015_IGLV_1nd.fasta
data-raw/IMGT_data/primers_raw/IGLV/Murugan2015_IGLV_1st.fasta
data-raw/IMGT_data/primers_raw/IGLV/Sblattero1998_IGLV.fasta
data-raw/IMGT_data/primers_raw/IGLV/Tiller2008_IGLV_1st.fasta
data-raw/IMGT_data/primers_raw/IGLV/Wardemann2003_IGLV_1st.fasta
data-raw/IMGT_primer_set_extractor.py
data-raw/Ippolito.R
data-raw/PCR_ref_data.xlsx
data-raw/RefCoverage.R data-raw/Tiller.R
data-raw/common_restriction_sites.txt
data-raw/sysdata.R
data/Comparison.rda
data/Ippolito.rda
data/RefCoverage.rda
data/Tiller.rda
inst/NEWS
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Brezinschek1995_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Brezinschek1995_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Cardona1995.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Chong2002.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Glamann1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Glas1999.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Ippolito2012.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Kueppers1993.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Lim2010.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Manheimer1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Marks1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Murugan2015_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Murugan2015_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Persson1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Rubinstein1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Sblattero1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Scheid2011.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Szczepa2001.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Tiller2008_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Tiller2008_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Verhagen2000.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Wardemann2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Weng1992.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_Wu2010.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_openPrimeR2017.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanDongen2003_A.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanDongen2003_B.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanDongen2003_C.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanDongen2003_single.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanEs1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH/IGH_vanEs1991_CDR.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGH_templates.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Atkinson1996.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Beishuizen1997.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Cardona1995.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Chen1986.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Chen1987.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Cox1994.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Giachino1995.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Glamann1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Huber1993.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Ippolito2012.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Juul1997.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Kueppers1993.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Lim2010.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Manheimer1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Marks1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Murugan2015_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Murugan2015_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Padyukov2001.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Persson1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Pongers1999.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Rubinstein1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Sblattero1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Tiller2008.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Timmers1993.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_Wardemann2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_openPrimeR2017.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_vanBurg2001.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_vanDongen2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK/IGK_vanEs1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGK_templates.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Cardona1995.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Farner1999_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Farner1999_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Ippolito2012.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Lim2010.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Marks1991.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Moraes2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Murugan2015_1st.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Murugan2015_2nd.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Rubinstein1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Sblattero1998.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Stiernholm1994.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Tiller2008.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_Wardemann2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_openPrimeR2017.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_vanBurg2001.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL/IGL_vanDongen2003.csv
inst/extdata/IMGT_data/comparison/primer_sets/IGL_templates.csv
inst/extdata/IMGT_data/comparison/templates/IGH_templates.csv
inst/extdata/IMGT_data/comparison/templates/IGK_templates.csv
inst/extdata/IMGT_data/comparison/templates/IGL_templates.csv
inst/extdata/IMGT_data/primers/IGHV/Brezinschek1995_1st.fasta
inst/extdata/IMGT_data/primers/IGHV/Brezinschek1995_2nd.fasta
inst/extdata/IMGT_data/primers/IGHV/Cardona1995.fasta
inst/extdata/IMGT_data/primers/IGHV/Chong2002.fasta
inst/extdata/IMGT_data/primers/IGHV/Glamann1998.fasta
inst/extdata/IMGT_data/primers/IGHV/Glas1999.fasta
inst/extdata/IMGT_data/primers/IGHV/Ippolito2012.fasta
inst/extdata/IMGT_data/primers/IGHV/Kueppers1993.fasta
inst/extdata/IMGT_data/primers/IGHV/Lim2010.fasta
inst/extdata/IMGT_data/primers/IGHV/Manheimer1991.fasta
inst/extdata/IMGT_data/primers/IGHV/Marks1991.fasta
inst/extdata/IMGT_data/primers/IGHV/Murugan2015_1st.fasta
inst/extdata/IMGT_data/primers/IGHV/Murugan2015_2nd.fasta
inst/extdata/IMGT_data/primers/IGHV/Persson1991.fasta
inst/extdata/IMGT_data/primers/IGHV/Rubinstein1998.fasta
inst/extdata/IMGT_data/primers/IGHV/Sblattero1998.fasta
inst/extdata/IMGT_data/primers/IGHV/Scheid2011.fasta
inst/extdata/IMGT_data/primers/IGHV/Szczepa2001.fasta
inst/extdata/IMGT_data/primers/IGHV/Tiller2008_1st.fasta
inst/extdata/IMGT_data/primers/IGHV/Tiller2008_2nd.fasta
inst/extdata/IMGT_data/primers/IGHV/Verhagen2000.fasta
inst/extdata/IMGT_data/primers/IGHV/Wardemann2003.fasta
inst/extdata/IMGT_data/primers/IGHV/Weng1992.fasta
inst/extdata/IMGT_data/primers/IGHV/Wu2010.fasta
inst/extdata/IMGT_data/primers/IGHV/openPrimeR2017.fasta
inst/extdata/IMGT_data/primers/IGHV/vanDongen2003_A.fasta
inst/extdata/IMGT_data/primers/IGHV/vanDongen2003_B.fasta
inst/extdata/IMGT_data/primers/IGHV/vanDongen2003_C.fasta
inst/extdata/IMGT_data/primers/IGHV/vanDongen2003_single.fasta
inst/extdata/IMGT_data/primers/IGHV/vanEs1991.fasta
inst/extdata/IMGT_data/primers/IGHV/vanEs1991_CDR.fasta
inst/extdata/IMGT_data/primers/IGKV/Atkinson1996.fasta
inst/extdata/IMGT_data/primers/IGKV/Beishuizen1997.fasta
inst/extdata/IMGT_data/primers/IGKV/Cardona1995.fasta
inst/extdata/IMGT_data/primers/IGKV/Chen1986.fasta
inst/extdata/IMGT_data/primers/IGKV/Chen1987.fasta
inst/extdata/IMGT_data/primers/IGKV/Cox1994.fasta
inst/extdata/IMGT_data/primers/IGKV/Giachino1995.fasta
inst/extdata/IMGT_data/primers/IGKV/Glamann1998.fasta
inst/extdata/IMGT_data/primers/IGKV/Huber1993.fasta
inst/extdata/IMGT_data/primers/IGKV/Ippolito2012.fasta
inst/extdata/IMGT_data/primers/IGKV/Juul1997.fasta
inst/extdata/IMGT_data/primers/IGKV/Kueppers1993.fasta
inst/extdata/IMGT_data/primers/IGKV/Lim2010.fasta
inst/extdata/IMGT_data/primers/IGKV/Manheimer1991.fasta
inst/extdata/IMGT_data/primers/IGKV/Marks1991.fasta
inst/extdata/IMGT_data/primers/IGKV/Murugan2015_1st.fasta
inst/extdata/IMGT_data/primers/IGKV/Murugan2015_2nd.fasta
inst/extdata/IMGT_data/primers/IGKV/Padyukov2001.fasta
inst/extdata/IMGT_data/primers/IGKV/Persson1991.fasta
inst/extdata/IMGT_data/primers/IGKV/Pongers1999.fasta
inst/extdata/IMGT_data/primers/IGKV/Rubinstein1998.fasta
inst/extdata/IMGT_data/primers/IGKV/Sblattero1998.fasta
inst/extdata/IMGT_data/primers/IGKV/Tiller2008.fasta
inst/extdata/IMGT_data/primers/IGKV/Timmers1993.fasta
inst/extdata/IMGT_data/primers/IGKV/Wardemann2003.fasta
inst/extdata/IMGT_data/primers/IGKV/openPrimeR2017.fasta
inst/extdata/IMGT_data/primers/IGKV/vanBurg2001.fasta
inst/extdata/IMGT_data/primers/IGKV/vanDongen2003.fasta
inst/extdata/IMGT_data/primers/IGKV/vanEs1991.fasta
inst/extdata/IMGT_data/primers/IGLV/Cardona1995.fasta
inst/extdata/IMGT_data/primers/IGLV/Farner1999_1st.fasta
inst/extdata/IMGT_data/primers/IGLV/Farner1999_2nd.fasta
inst/extdata/IMGT_data/primers/IGLV/Ippolito2012.fasta
inst/extdata/IMGT_data/primers/IGLV/Lim2010.fasta
inst/extdata/IMGT_data/primers/IGLV/Marks1991.fasta
inst/extdata/IMGT_data/primers/IGLV/Moraes2003.fasta
inst/extdata/IMGT_data/primers/IGLV/Murugan2015_1st.fasta
inst/extdata/IMGT_data/primers/IGLV/Murugan2015_2nd.fasta
inst/extdata/IMGT_data/primers/IGLV/Rubinstein1998.fasta
inst/extdata/IMGT_data/primers/IGLV/Sblattero1998.fasta
inst/extdata/IMGT_data/primers/IGLV/Stiernholm1994.fasta
inst/extdata/IMGT_data/primers/IGLV/Tiller2008.fasta
inst/extdata/IMGT_data/primers/IGLV/Wardemann2003.fasta
inst/extdata/IMGT_data/primers/IGLV/openPrimeR2017.fasta
inst/extdata/IMGT_data/primers/IGLV/vanBurg2001.fasta
inst/extdata/IMGT_data/primers/IGLV/vanDongen2003.fasta
inst/extdata/IMGT_data/primers/Test/test_both.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_any_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_any_leader.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_functional_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_functional_exon_exp.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_functional_leader.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGH_functional_leader_exp.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGK_any_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGK_any_leader.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGK_functional_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGK_functional_leader.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGL_any_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGL_any_leader.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGL_functional_exon.fasta
inst/extdata/IMGT_data/templates/Homo_sapiens_IGL_functional_leader.fasta
inst/extdata/Vir/HIV-1/gag/comparison/primers/Wei2004.csv
inst/extdata/Vir/HIV-1/gag/comparison/templates/HIV1_REF_2010_gag_DNA.csv
inst/extdata/Vir/HIV-1/gag/primers/Wei2004.fasta
inst/extdata/Vir/HIV-1/gag/templates/.HIV1_REF_2010_gag_DNA.fasta.swp
inst/extdata/Vir/HIV-1/gag/templates/HIV1_REF_2010_gag_DNA.fasta
inst/extdata/Vir/HIV-1/pol/comparison/primers/Dudley_2014.csv
inst/extdata/Vir/HIV-1/pol/comparison/primers/Nie2011.csv
inst/extdata/Vir/HIV-1/pol/comparison/templates/pol.csv
inst/extdata/Vir/HIV-1/pol/primers/Dudley2014.fasta
inst/extdata/Vir/HIV-1/pol/primers/Nie2011.fasta
inst/extdata/Vir/HIV-1/pol/templates/HIV1_REF_2010_pol_DNA.fasta
inst/extdata/report/disclaimer.Rmd
inst/extdata/report/header.tex
inst/extdata/report/logo_text.png
inst/extdata/report/parameters.Rmd inst/extdata/report/report.Rmd inst/extdata/report/report_comparison.Rmd
inst/extdata/settings/A_Taq_PCR_design.xml
inst/extdata/settings/B_Taq_PCR_evaluate.xml
inst/extdata/settings/C_Taq_PCR_high_stringency.xml
inst/extdata/settings/settings_schema.xsd
inst/tutorials/introduction/compare_primers.Rmd inst/tutorials/introduction/designing_primers.Rmd inst/tutorials/introduction/evaluate_constraints.Rmd inst/tutorials/introduction/introduction.Rmd
inst/tutorials/introduction/introduction.html
inst/tutorials/introduction/loading_primers.Rmd inst/tutorials/introduction/loading_settings.Rmd inst/tutorials/introduction/loading_templates.Rmd inst/tutorials/introduction/preliminaries.Rmd inst/tutorials/introduction/primer_coverage.Rmd man/AnalysisStats.Rd man/Data.Rd man/Input.Rd man/Output.Rd man/Plots.Rd man/PrimerDesign.Rd man/PrimerEval.Rd man/Primers-method.Rd man/Scoring.Rd man/Settings.Rd man/Templates-method.Rd man/TemplatesFunctions.Rd man/check_cvg_constraints.Rd man/create_report-Primers-Templates-method.Rd man/create_report-list-list-method.Rd man/filterLimits-methods.Rd man/filters-methods.Rd man/get_cvg_stats-Primers-method.Rd man/get_cvg_stats-list-method.Rd man/openPrimeR-package.Rd man/plot_constraint-Primers-method.Rd man/plot_constraint-list-method.Rd man/plot_constraint_deviation-Primers-method.Rd man/plot_constraint_deviation-list-method.Rd man/plot_constraint_fulfillment-Primers-method.Rd man/plot_constraint_fulfillment-list-method.Rd man/plot_cvg_constraints-Primers-method.Rd man/plot_cvg_constraints-list-method.Rd man/plot_primer_binding_regions-Primers-Templates-method.Rd man/plot_primer_binding_regions-list-list-method.Rd man/plot_primer_cvg-Primers-Templates-method.Rd man/plot_primer_cvg-list-list-method.Rd man/plot_template_cvg-Primers-Templates-method.Rd man/plot_template_cvg-list-list-method.Rd man/runTutorial.Rd tests/testthat.R tests/testthat/load_test_data.R tests/testthat/test_IO.R tests/testthat/test_con_dimerization.R tests/testthat/test_con_gc.R tests/testthat/test_con_primer_coverage.R tests/testthat/test_con_primer_length.R tests/testthat/test_con_primer_specificity.R tests/testthat/test_con_repeats_runs.R tests/testthat/test_con_secondary_structure.R tests/testthat/test_primer_comparison.R tests/testthat/test_primer_design.R tests/testthat/test_primers.R tests/testthat/test_settings.R tests/testthat/test_templates.R vignettes/openPrimeR_vignette.Rmd
matdoering/openPrimeR documentation built on Dec. 28, 2019, 7:08 p.m.