https://impilo.diploide.net/ 2026-05-01T18:27:24+00:00 https://impilo.diploide.net/ https://impilo.diploide.net/lib/exe/fetch.php?media=wiki:logo.png text/html 2026-01-29T21:42:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:altschul_sf_1990&rev=1769722933&do=diff Note name :altschul_s_1990 Authors Altschul S.F., Gish W., Miller W., Myers E.W. & Lipman, D.J.Title Basic local alignment search tool.Journal J. Mol. Biol.Volume 215Published1990Pages 403-410URL <https://www.ncbi.nlm.nih.gov/pubmed/2231712?dopt=Citation> text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:berriman_m_2003&rev=1622316954&do=diff Note name :ref:berriman_m_2003 Authors Berriman, M & Rutherford, K. Title Viewing and annotating sequence data with Artemis. Journal Briefings in bioinformatics Volume 4 Published 2003 Pages 124-132 URL <http://europepmc.org/abstract/MED/12846394> text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:bioc_url_db&rev=1622316954&do=diff Note name :bioc_affy_qc Note text affy: Methods for Affymetrix Oligonucleotide Arrays URL <http://www.bioconductor.org/packages/release/bioc/html/affy.html> Note name :bioc_affyPLM_qc Note text affyPLM: Model Based QC Assessment of Affymetrix GeneChips URL <http://bioconductor.org/packages/2.6/bioc/html/affyPLM.html> Note name :bioc_affyPLM_model text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:bolger_2014&rev=1622316954&do=diff Note name bolger_am_2014 Authors Bolger, A. M., Lohse, M. & Uradel, B. Title Trimmomatic: a flexible trimmer for Illumina sequence data. Journal Bioinformatics Volume 30(15) Published 2014 Pages 2114-2120 URL <https://academic.oup.com/bioinformatics/article/30/15/2114/2390096> text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:brazma_a_2000&rev=1622316954&do=diff Note name :ref:brazma_a_2000 Authors Brazma, A., Robinson A., Cameron G. & Ashburner, M. Title One-stop shop for microarray data Journal Nature Volume 403 Published 2000 Pages 699-700 URL <http://www.nature.com/nature/journal/v403/n6771/full/403699a0.html> text/html 2024-07-12T19:39:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:carver_t_2008&rev=1720813145&do=diff Note name :carver_t_2008 Authors Carver T, Berriman M, Tivey A, Patel C, Böhme U, Barrel, B. G., Parkhill, J. & Rajandream, M.A. Title Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database. Journal text/html 2024-07-12T19:38:55+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:carver_t_2012&rev=1720813135&do=diff Note name :carver_t_2012 Authors Carver T., Harris S. R., Berriman M., Parkhill J. & McQuillan J. A. Title Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data. Journal Bioinformatics text/html 2024-11-21T18:28:19+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:chen_s_2018&rev=1732213699&do=diff Note name chen_s_2018 Authors Chen, S., Zhou, Y., Chen, Y. & Gu, J. Title fastp: an ultra-fast all-in-one FASTQ preprocessor Journal Bioinformatics Volume 34 Published 2018 Pages i884–i890 URL <https://academic.oup.com/bioinformatics/article/34/17/i884/5093234> text/html 2024-11-21T18:28:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:chen_s_2023&rev=1732213713&do=diff Note name chen_s_2023 Authors Chen, S. Title Ultrafast one-pass FASTQ data preprocessing, quality control, and deduplication using fastp Journal iMeta Volume 2 Published 2023 Pages e107 URL <https://onlinelibrary.wiley.com/doi/10.1002/imt2.107> text/html 2025-05-15T13:32:36+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:grabherr_mg_2011&rev=1747315956&do=diff Note name :grabherr_mg_2011 Authors Grabherr M.G., Haas B.J., Yassour M., Levin J.Z., Thompson D.A., Amit I., Adiconis X., Fan L., Raychowdhury R., Zeng Q., Chen Z., Mauceli E., Hacohen N., Gnirke A., Rhind N., di Palma F., Birren B.W., Nusbaum C., Lindblad-Toh K., Friedman N. & Regev A. text/html 2025-05-15T13:30:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:haas_bj_2013&rev=1747315833&do=diff Note name :haas_bj_2013 Authors Haas B.J.., Papanicolaou A., Yassour M., Grabherr M., Blood P.D., Bowden J., Couger M.B., Eccles D., Li B., Lieber M., MacManes M.D., Ott M., Orvis J., Pochet N., Strozzi F., Weeks N., Westerman R., William T., Dewey C.N., Henschel R., LeDuc R.D., Friedman N. & Regev A. text/html 2024-07-13T13:08:17+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:higgins_dg_1988&rev=1720876097&do=diff Note name :higgins_dg_1988 Author D. G. Higgins and P. M. Sharp Title CLUSTAL: a package for performing multiple sequence alignment on a microcomputer Journal Gene Volume 73 Published 1988 Pages 237-244 URL <https://pubmed.ncbi.nlm.nih.gov/3243435/> text/html 2026-01-29T21:41:02+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:himes_be_2014&rev=1769722862&do=diff Note name :himes_be_2014 Authors Himes, B.E., Jiang, .X, Wagner, P., Hu. R., Wang, Q., Klanderman, B., Whitaker, R.M., Duan, Q., Lasky-Su, J., Nikolos C., Jester, W., Johnson, M., Panettieri, R.A. Jr, Tantisira, K.G., Weiss, S.T., Lu Q.Title RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells. text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:kaufmann_a_2010_1&rev=1622316954&do=diff Note name :kaufmann_a_2010_1 Authors Kaufmann, A. & Huber,W. Title Microarray data quality control improves the detection of differentially expressed genes Journal Genomics Volume 95 Published 2010 Pages 138 - 142 URL text/html 2021-06-05T14:08:13+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:krumsiek_j_2007&rev=1622902093&do=diff Note name :krumsiek_j_2007 Authors Jan Krumsiek, Roland Arnold & Thomas Rattei Title Gepard: a rapid and sensitive tool for creating dotplots on genome scale. Journal Bioinformatics Volume 23 Published 2007 Pages 1026–1028 text/html 2024-07-13T13:14:06+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:larkin_ma_2007&rev=1720876446&do=diff Note name :larkin_ma_2007 Author M. A. Larkin, G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan, H. McWilliam, F. Valentin, I. M. Wallace, A. Wilm, R. Lopez, J. D. Thompson, T. J. Gibson and D G Higgins Title Clustal W and Clustal X version 2.0 text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:lin_2008&rev=1622316954&do=diff Note name :ref:Lin_2008 Authors Lin, S.M., Du, P. and Kibbe,W.A Title Model-Based Variance-stabilizing Transformation for Illumina Microarray Data. Journal Nucleic Acids Research Volume 36 Published 2008 Pages e11 URL text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:liu_2001&rev=1622316954&do=diff Note name :ref:Liu_2001 Authors Liu, W., Mei, R., Bartell, D. M., Di, X., Webster, T. A. and Ryder, T. Title Rank-based algorithms for analysis of microarrays. Journal Proceedings of SPIE Volume Microarrays: Optical Technologies and Informatics text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:liu_2002&rev=1622316954&do=diff Note name :ref:Liu_2002 Authors Liu, W. M., Mei, R., Di, X., Ryder, T. B., Hubbell, E., Dee, S., Webster, T. A., Harrington, C. A., Ho, M. H., Baid, J., Smeekens, S. P. Title Analysis of high density expression microarrays with signed-rank call algorithms. text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:mullan_lj_2002&rev=1622316954&do=diff Note name :ref:mullan_lj_2002 Authors Mullan, L. J. & Bleasby, A. Title Short EMBOSS User Guide Journal Briefs Bioinform Volume 3 Published 2002 Pages 92-94 URL <http://bib.oxfordjournals.org/content/3/1/92.long> text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:patro_r_2017&rev=1622316954&do=diff Note name :patro_r_2017 Authors Patro, R, Duggal, G, Love, M. I., Irizarry, R. A. & Kingsford, C. Title Salmon provides fast and bias-aware quantification of transcript expression. Journal Nature Methods Volume 14 Published 2017 text/html 2024-07-12T19:51:26+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_1988&rev=1720813886&do=diff Note name :pearson_wr_1988 Author W. R. Pearson and D. J. Lipman Title Improved tools for biological sequence comparison Journal Proc. Natl. Acad. Sci. USA Volume 85 Published 1988 Pages 2444-2448 URL <https://pubmed.ncbi.nlm.nih.gov/3162770/> text/html 2024-07-12T19:51:05+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_1996&rev=1720813865&do=diff Note name :pearson_wr_1996 Author W. R. Pearson Title Effective protein sequence comparison Journal Methods Enzymol. Volume 266 Published 1996: Pages 227-258 URL <https://pubmed.ncbi.nlm.nih.gov/8743688/> text/html 2024-07-12T19:54:20+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_1997&rev=1720814060&do=diff Note name :pearson_wr_1997 Author W. R. Pearson, T. Wood, Z. Zhang and W. Miller Title Comparison of DNA sequences with protein sequences Journal Genomics Volume 46 Published 1997 Pages 24-36 URL <https://pubmed.ncbi.nlm.nih.gov/9403055/> text/html 2024-07-12T19:57:09+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_2000&rev=1720814229&do=diff Note name :pearson_wr_2000 Author W. R. Pearson Title Flexible sequence similarity searching with the FASTA3 program package Journal Methods Mol. Biol. Volume 132 Published 2000 Pages 185-219 URL <https://pubmed.ncbi.nlm.nih.gov/10547837/> text/html 2024-07-12T20:04:32+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_2013&rev=1720814672&do=diff Note name :pearson_wr_2013 Author W. R. Pearson Title Selecting the Right Similarity-Scoring Matrix Journal Curr. Protoc. Bioinformatics Volume 43 Published 2013 Pages 3.5.1-3.5.9 URL <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3848038/> text/html 2024-07-12T20:06:08+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pearson_wr_2016&rev=1720814768&do=diff Note name :pearson_wr_2016 Author W. R. Pearson Title Finding Protein and Nucleotide Similarities with FASTA Journal Curr. Protoc. Bioinformatics Volume 53 Published 2016 Pages 3.9.1-3.9.25 URL <https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5072362/> text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pertea_m_2015&rev=1622316954&do=diff Note name :ref:pertea_m_2015 Authors Pertea M., Pertea G. M., Antonescu C. M., Chang T. C., Mendell J. T. & Salzberg S. L. Title StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Journal Nature Biotechnology text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:pertea_m_2016&rev=1622316954&do=diff Note name :ref:pertea_m_2016 Authors Pertea M., Kim D., Pertea G. M., Leek J. T. & Salzberg S. L. Title Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Journal Nature Protocols Volume text/html 2024-11-22T15:19:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:prjibelski_a_2020&rev=1732288765&do=diff Note name prjibelski_a_2020 Author Prjibelski, A., Antipov, D., Meleshko, D., Lapidus, A., & Korobeynikov, A. Title Using SPAdes De Novo Assembler Journal Curr. Prot. Bioinformatics Volume 70 Published 2020 Pages e102 text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:rice_p_2000&rev=1622316954&do=diff Note name :ref:rice_p_2000 Authors Rice, P., Longden, I. & Bleasby, A. Title EMBOSS: the European Molecular Biology Open Software Suite. Journal Trends in Genetics Volume 16 Published 2000 Pages 276-277 text/html 2024-07-12T19:18:43+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:robinson_jt_2011&rev=1720811923&do=diff Note name :robinson_jt_2011 Author James T. Robinson, Helga Thorvaldsdóttir, Wendy Winckler, Mitchell Guttman, Eric S. Lander, Gad Getz and Jill P. Mesirov Title Integrative Genome Viewer Journal Nature Biotechnol. Volume 29 Published text/html 2021-05-29T19:35:54+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:rutherford_k_2000&rev=1622316954&do=diff Note name :ref:rutherford_k_2000 Authors Rutherford, K., Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA and Barrell B Title Artemis: sequence visualization and annotation. Journal Bioinformatics Volume 16 Published 2000 text/html 2024-07-13T13:25:25+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:sievers_f_2011&rev=1720877125&do=diff Note name :sievers_f_2011 Author F. Sievers, A. Wilm, D. Dineen, T. J. Gibson, K. Karplus, W. Li, R. Lopez, H. McWilliam, M. Remmert, J. Söding, J. D. Thompson and D. G. Higgins Title Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega text/html 2024-07-13T13:42:56+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:sievers_f_2014&rev=1720878176&do=diff Note name :sievers_f_2014 Author F. Sievers and D. G. Higgins Title Clustal Omega Journal Curr. Protoc. Bioinformatics Volume 48 Published 2014 Pages 3.13.1-3.13.16 URL <https://pubmed.ncbi.nlm.nih.gov/25501942/> text/html 2024-07-13T13:28:33+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:sievers_f_2017&rev=1720877313&do=diff Note name :sievers_f_2017 Author F. Sievers and D. G. Higgins Title Clustal Omega for making accurate alignments of many protein sequences Journal Protein Sci. Volume 27 Published 2018 Pages 135-145 URL <https://onlinelibrary.wiley.com/doi/full/10.1002/pro.3290> text/html 2024-07-12T19:23:21+00:00 Anonymous (anonymous@undisclosed.example.com) https://impilo.diploide.net/doku.php?id=refnotes:thorvaldsdottir_h_2013&rev=1720812201&do=diff Note name :thorvaldsdottir_h_2013 Author Helga Thorvaldsdóttir, James T. Robinson and Jill P. Mesirov Title Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration Journal Briefings in Bioinformatics