User contributions
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- 14:18, 9 May 2017 (diff | hist) . . (0) . . File:Htseq.png (Rf uploaded a new version of File:Htseq.png) (current)
- 14:18, 9 May 2017 (diff | hist) . . (0) . . N File:Htcats.png (Uploaded with SimpleBatchUpload) (current)
- 14:14, 9 May 2017 (diff | hist) . . (-401) . . Estimating Gene Count Talk
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:Htseq.png (Uploaded with SimpleBatchUpload)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:Htcats.png.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:T1t2t3aggreg.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:T1t2t3.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:Unsolved.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:T1t2aggreg.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:T1.png (Uploaded with SimpleBatchUpload) (current)
- 14:13, 9 May 2017 (diff | hist) . . (0) . . N File:T1t2.png (Uploaded with SimpleBatchUpload) (current)
- 13:33, 9 May 2017 (diff | hist) . . (+2,175) . . N Estimating Gene Count Talk (Created page with "Estimating gene count = Estimating Gene Count = How many reads are overlapping genomic features? - or - Can we confidently assign each read to a feature/transcript/gene? Not...")
- 13:22, 9 May 2017 (diff | hist) . . (-13) . . Quality of Mapping Talk (current)
- 13:20, 9 May 2017 (diff | hist) . . (-17) . . Quality of Mapping Talk
- 13:20, 9 May 2017 (diff | hist) . . (+17) . . Quality of Mapping Talk
- 13:15, 9 May 2017 (diff | hist) . . (+1,328) . . N Quality of Mapping Talk (Created page with "= Mapping quality control = Some issues are only detectable in the context of the genome: * Duplicate reads * Fragment size distribution * Gene coverage * Completeness of data...")
- 12:49, 9 May 2017 (diff | hist) . . (0) . . N File:Gcov.png (Uploaded with SimpleBatchUpload) (current)
- 12:49, 9 May 2017 (diff | hist) . . (0) . . N File:Inssz.png (Uploaded with SimpleBatchUpload) (current)
- 12:49, 9 May 2017 (diff | hist) . . (0) . . N File:Comp.png (Uploaded with SimpleBatchUpload) (current)
- 12:49, 9 May 2017 (diff | hist) . . (0) . . N File:Dups.png (Uploaded with SimpleBatchUpload) (current)
- 12:33, 9 May 2017 (diff | hist) . . (+58) . . Quality Control and Preprocessing Exercise
- 12:31, 9 May 2017 (diff | hist) . . (+129) . . Quality Control and Preprocessing Exercise
- 11:39, 9 May 2017 (diff | hist) . . (0) . . File:Biorpaper.png (Rf uploaded a new version of File:Biorpaper.png) (current)
- 11:39, 9 May 2017 (diff | hist) . . (0) . . File:Rnasoc.png (Rf uploaded a new version of File:Rnasoc.png) (current)
- 11:28, 9 May 2017 (diff | hist) . . (0) . . N File:Igvlayout.png (Uploaded with SimpleBatchUpload) (current)
- 11:28, 9 May 2017 (diff | hist) . . (0) . . N File:Rnasoc.png (Uploaded with SimpleBatchUpload)
- 11:28, 9 May 2017 (diff | hist) . . (0) . . N File:Biorpaper.png (Uploaded with SimpleBatchUpload)
- 11:27, 9 May 2017 (diff | hist) . . (+189) . . RNASeq library preparation (current)
- 11:11, 9 May 2017 (diff | hist) . . (+55) . . Visualisation of mapped reads
- 10:32, 9 May 2017 (diff | hist) . . (-3) . . RNASeq library preparation
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Dan.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Illu.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Illu2.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Totalrna.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Illu5.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Rnawf.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Illu4.png (Uploaded with SimpleBatchUpload) (current)
- 10:24, 9 May 2017 (diff | hist) . . (0) . . N File:Illu3.png (Uploaded with SimpleBatchUpload) (current)
- 10:23, 9 May 2017 (diff | hist) . . (+787) . . N RNASeq library preparation (Created page with "= Total RNA = File:totalrna.png = mRNA-seq workflow = File:rnawf.png = Illumina NGS Library = File:illu.png = Illumina library read binding 1= File:illu2....")
- 00:19, 9 May 2017 (diff | hist) . . (+13) . . Mapping to Reference Talk (current)
- 00:16, 9 May 2017 (diff | hist) . . (-507) . . Mapping to Reference Talk
- 00:13, 9 May 2017 (diff | hist) . . (0) . . N File:Optags2.png (Uploaded with SimpleBatchUpload) (current)
- 00:13, 9 May 2017 (diff | hist) . . (0) . . N File:Optags1.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Alignsec.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Sam2panel.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Headersec.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Cigarex.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Flag.png (Uploaded with SimpleBatchUpload) (current)
- 00:12, 9 May 2017 (diff | hist) . . (0) . . N File:Cigar.png (Uploaded with SimpleBatchUpload) (current)
- 23:31, 8 May 2017 (diff | hist) . . (0) . . N File:Hist.png (Uploaded with SimpleBatchUpload) (current)
- 23:31, 8 May 2017 (diff | hist) . . (0) . . N File:Mappers.png (Uploaded with SimpleBatchUpload) (current)
- 23:31, 8 May 2017 (diff | hist) . . (0) . . N File:Vital.png (Uploaded with SimpleBatchUpload) (current)
- 23:31, 8 May 2017 (diff | hist) . . (0) . . N File:Mapproc.png (Uploaded with SimpleBatchUpload) (current)
- 23:30, 8 May 2017 (diff | hist) . . (-374) . . Mapping to Reference Talk
- 23:18, 8 May 2017 (diff | hist) . . (+6) . . Quality Control and Preprocessing Talk
- 23:16, 8 May 2017 (diff | hist) . . (0) . . N File:Sdl3.png (Uploaded with SimpleBatchUpload) (current)
- 23:16, 8 May 2017 (diff | hist) . . (0) . . File:Sf1.png (Rf uploaded a new version of File:Sf1.png) (current)
- 23:14, 8 May 2017 (diff | hist) . . (0) . . File:Psnc3.png (Rf uploaded a new version of File:Psnc3.png) (current)
- 23:08, 8 May 2017 (diff | hist) . . (0) . . N File:Sf1.png (Uploaded with SimpleBatchUpload)
- 23:06, 8 May 2017 (diff | hist) . . (0) . . N File:Ptsq4.png (Uploaded with SimpleBatchUpload) (current)
- 23:06, 8 May 2017 (diff | hist) . . (0) . . N File:Bimods.png (Uploaded with SimpleBatchUpload) (current)
- 23:06, 8 May 2017 (diff | hist) . . (0) . . N File:Ptsq3.png (Uploaded with SimpleBatchUpload) (current)
- 23:05, 8 May 2017 (diff | hist) . . (0) . . N File:Gff.png (Uploaded with SimpleBatchUpload) (current)
- 23:04, 8 May 2017 (diff | hist) . . (0) . . N File:Psnc3.png (Uploaded with SimpleBatchUpload)
- 23:04, 8 May 2017 (diff | hist) . . (0) . . N File:Pbgcc3.png (Uploaded with SimpleBatchUpload) (current)
- 23:04, 8 May 2017 (diff | hist) . . (0) . . N File:Ovrep3.png (Uploaded with SimpleBatchUpload) (current)
- 23:03, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsqb3.png (Uploaded with SimpleBatchUpload) (current)
- 23:03, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsc3.png (Uploaded with SimpleBatchUpload) (current)
- 23:03, 8 May 2017 (diff | hist) . . (0) . . N File:Psgcc3.png (Uploaded with SimpleBatchUpload) (current)
- 23:03, 8 May 2017 (diff | hist) . . (0) . . File:Pbsqb4.png (Rf uploaded a new version of File:Pbsqb4.png) (current)
- 23:02, 8 May 2017 (diff | hist) . . (-2,891) . . Quality Control and Preprocessing Talk
- 22:28, 8 May 2017 (diff | hist) . . (+1) . . Visualisation of mapped reads
- 21:45, 8 May 2017 (diff | hist) . . (+665) . . I2rda Course Cheatsheet
- 21:25, 8 May 2017 (diff | hist) . . (+53) . . Visualisation of mapped reads
- 21:23, 8 May 2017 (diff | hist) . . (-61) . . Visualisation of mapped reads
- 19:38, 8 May 2017 (diff | hist) . . (+144) . . Visualisation of mapped reads
- 19:34, 8 May 2017 (diff | hist) . . (+3,569) . . N Visualisation of mapped reads (Created page with "= Introduction = In contrast to the other more quantitative stages, this exercise is qualitative in the sense that we get a visual feel for a certain area of interest. = Aim...")
- 19:24, 8 May 2017 (diff | hist) . . (+1) . . Quality of Mapping Exercise
- 19:17, 8 May 2017 (diff | hist) . . (+830) . . Quality of Mapping Exercise
- 18:43, 8 May 2017 (diff | hist) . . (+52) . . I2rda Course Cheatsheet
- 18:37, 8 May 2017 (diff | hist) . . (+423) . . I2rda Course Cheatsheet
- 16:02, 8 May 2017 (diff | hist) . . (+204) . . Quality Control and Preprocessing Exercise
- 12:19, 8 May 2017 (diff | hist) . . (0) . . Quality Control and Preprocessing Talk
- 12:18, 8 May 2017 (diff | hist) . . (-1) . . Quality Control and Preprocessing Talk
- 12:17, 8 May 2017 (diff | hist) . . (-28) . . Quality Control and Preprocessing Talk
- 12:17, 8 May 2017 (diff | hist) . . (+1) . . Quality Control and Preprocessing Talk
- 12:15, 8 May 2017 (diff | hist) . . (0) . . Quality Control and Preprocessing Talk
- 12:14, 8 May 2017 (diff | hist) . . (+29) . . Quality Control and Preprocessing Talk
- 12:13, 8 May 2017 (diff | hist) . . (-1) . . Quality Control and Preprocessing Talk
- 12:09, 8 May 2017 (diff | hist) . . (+142) . . Quality Control and Preprocessing Talk
- 12:06, 8 May 2017 (diff | hist) . . (+131) . . Quality Control and Preprocessing Talk
- 12:05, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsqb4.png
- 11:54, 8 May 2017 (diff | hist) . . (0) . . N File:Multiqc.png (current)
- 01:41, 8 May 2017 (diff | hist) . . (0) . . N File:Ngsqc.png (Uploaded with SimpleBatchUpload) (current)
- 01:41, 8 May 2017 (diff | hist) . . (0) . . N File:Fastqc.png (Uploaded with SimpleBatchUpload) (current)
- 01:41, 8 May 2017 (diff | hist) . . (0) . . N File:Fastx.png (Uploaded with SimpleBatchUpload) (current)
- 01:41, 8 May 2017 (diff | hist) . . (0) . . N File:Fformat.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Ptsq2.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Ptsq.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Sf.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Sf2.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Psqs.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Psnc.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Sdl.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Psgcc.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Sascha.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Ovrep.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsc.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsqb.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Pbgcc.png (Uploaded with SimpleBatchUpload) (current)
- 01:37, 8 May 2017 (diff | hist) . . (0) . . N File:Pbsqg.png (Uploaded with SimpleBatchUpload) (current)
- 01:30, 8 May 2017 (diff | hist) . . (0) . . N File:Ascii.png (current)
- 01:28, 8 May 2017 (diff | hist) . . (+6,858) . . N Quality Control and Preprocessing Talk (Created page with "Quality control and data pre-processing = Contents = * Data formats : – Fasta and Fastq formats : – Sequence quality encoding * Quality Control (QC) :– Evaluation of s...")
- 01:27, 8 May 2017 (diff | hist) . . (+6,858) . . N Quality Control Preprocessing Talk (Created page with "Quality control and data pre-processing = Contents = * Data formats : – Fasta and Fastq formats : – Sequence quality encoding * Quality Control (QC) :– Evaluation of s...") (current)
- 01:27, 8 May 2017 (diff | hist) . . (+6,858) . . N Quality and Control Preprocessing Talk (Created page with "Quality control and data pre-processing = Contents = * Data formats : – Fasta and Fastq formats : – Sequence quality encoding * Quality Control (QC) :– Evaluation of s...") (current)
- 01:16, 8 May 2017 (diff | hist) . . (+27) . . Quality of Mapping Exercise
- 21:22, 7 May 2017 (diff | hist) . . (-1) . . I2rda Course Cheatsheet
- 19:34, 7 May 2017 (diff | hist) . . (+398) . . I2rda Course Cheatsheet
- 19:26, 7 May 2017 (diff | hist) . . (-16) . . Quality of Mapping Exercise
- 19:23, 7 May 2017 (diff | hist) . . (0) . . Quality of Mapping Exercise
- 19:15, 7 May 2017 (diff | hist) . . (0) . . Quality of Mapping Exercise
- 19:14, 7 May 2017 (diff | hist) . . (+312) . . Quality of Mapping Exercise
- 19:13, 7 May 2017 (diff | hist) . . (+92) . . I2rda Course Cheatsheet
- 19:12, 7 May 2017 (diff | hist) . . (+164) . . I2rda Course Cheatsheet
- 19:10, 7 May 2017 (diff | hist) . . (+39) . . I2rda Course Cheatsheet
- 19:09, 7 May 2017 (diff | hist) . . (-1) . . I2rda Course Cheatsheet
- 19:08, 7 May 2017 (diff | hist) . . (+462) . . I2rda Course Cheatsheet
- 19:05, 7 May 2017 (diff | hist) . . (-1) . . I2rda Course Cheatsheet
- 19:04, 7 May 2017 (diff | hist) . . (+33) . . I2rda Course Cheatsheet
- 19:02, 7 May 2017 (diff | hist) . . (-1,673) . . I2rda Course Cheatsheet
- 18:56, 7 May 2017 (diff | hist) . . (+213) . . I2rda Course Cheatsheet
- 18:54, 7 May 2017 (diff | hist) . . (-16,925) . . I2rda Course Cheatsheet
- 18:44, 7 May 2017 (diff | hist) . . (+23,298) . . N I2rda Course Cheatsheet (Created page with "= The Command-line (shell) = The real power of Linux/Unix systems is the command line. * Many programs and facilities are available through graphical options on Linux, but a...")
- 18:26, 7 May 2017 (diff | hist) . . (+447) . . Quality of Mapping Exercise
- 18:21, 7 May 2017 (diff | hist) . . (0) . . m Quality of Mapping Exercise (Rf moved page Quality of Mapping to Quality of Mapping Exercise)
- 18:21, 7 May 2017 (diff | hist) . . (+41) . . N Quality of Mapping (Rf moved page Quality of Mapping to Quality of Mapping Exercise) (current)
- 18:10, 7 May 2017 (diff | hist) . . (+370) . . Intro to RNA-Seq Data Analysis Course
- 17:51, 7 May 2017 (diff | hist) . . (+27) . . Tophat (current)
- 17:49, 7 May 2017 (diff | hist) . . (+17) . . Main Page
- 17:47, 7 May 2017 (diff | hist) . . (+947) . . Tophat
- 17:35, 7 May 2017 (diff | hist) . . (+372) . . N Tophat (Created page with "Introduction = The well known sloice-aware aligner or mapper, now being phased out in favour of HISAT2 = Usage = module load tophat This will load the latest version (2.1...")
- 17:21, 7 May 2017 (diff | hist) . . (+41) . . Mapping to Reference Exercise
- 17:18, 7 May 2017 (diff | hist) . . (+2,370) . . Mapping to Reference Exercise
- 15:52, 7 May 2017 (diff | hist) . . (+99) . . Mapping to Reference Exercise
- 15:52, 7 May 2017 (diff | hist) . . (+2,460) . . Mapping to Reference (current)
- 15:13, 7 May 2017 (diff | hist) . . (+165) . . Intro to RNA-Seq Data Analysis Course
- 14:16, 7 May 2017 (diff | hist) . . (+84) . . Intro to RNA-Seq Data Analysis Course
- 14:12, 7 May 2017 (diff | hist) . . (+10) . . Intro to RNA-Seq Data Analysis Course
- 14:11, 7 May 2017 (diff | hist) . . (+304) . . Intro to RNA-Seq Data Analysis Course
- 14:07, 7 May 2017 (diff | hist) . . (-894) . . Intro to RNA-Seq Data Analysis Course
- 13:43, 7 May 2017 (diff | hist) . . (+2,891) . . Intro to RNA-Seq Data Analysis Course
- 13:22, 7 May 2017 (diff | hist) . . (+4,181) . . N Mapping to Reference Talk (Created page with "Mapping to a reference genome = Contents = * Overview * Mapping process: Algorithms and tools * Mapping output: SAM/BAM specification Mapping to a reference genome U Trived...")
- 19:52, 6 May 2017 (diff | hist) . . (+32) . . N I2rda mqx (Rf moved page I2rda mqx to Quality of Mapping) (current)
- 19:52, 6 May 2017 (diff | hist) . . (0) . . m Quality of Mapping Exercise (Rf moved page I2rda mqx to Quality of Mapping)
- 16:48, 6 May 2017 (diff | hist) . . (+6) . . Mapping to Reference Exercise
- 16:40, 6 May 2017 (diff | hist) . . (-54) . . Mapping to Reference Exercise
- 16:17, 6 May 2017 (diff | hist) . . (+2,433) . . N Mapping to Reference Exercise (Created page with "= Aims = Mapping to a reference genome is a vital step to generate counts and do differential gene expression thereafter. For RNA-Seq data it is important to choose an aligne...")
- 16:35, 5 May 2017 (diff | hist) . . (+96) . . m Quality Control and Preprocessing Exercise
- 16:33, 5 May 2017 (diff | hist) . . (+36) . . Quality Control and Preprocessing Exercise
- 15:05, 5 May 2017 (diff | hist) . . (+400) . . Quality Control and Preprocessing Exercise
- 14:30, 5 May 2017 (diff | hist) . . (+287) . . Quality Control and Preprocessing Exercise
- 14:25, 5 May 2017 (diff | hist) . . (+1) . . Ea-utils (current)
- 14:23, 5 May 2017 (diff | hist) . . (+681) . . Ea-utils
- 13:36, 5 May 2017 (diff | hist) . . (+4,220) . . N Ea-utils (Created page with "= Usage of Cluster= * Cluster Manual * Why a Queue Manager? * Available Software = Documented Programs = The following can be seen as extra notes referring to th...")
- 13:35, 5 May 2017 (diff | hist) . . (+16) . . Main Page
- 12:48, 5 May 2017 (diff | hist) . . (-165) . . Quality Control and Preprocessing Exercise
- 09:47, 5 May 2017 (diff | hist) . . (+7,908) . . N Differential Expression Talk (Created page with "07 Differential expression analysis = Goals = Three overall: Primarily, it's about: * Identify differentially expressed genes in two or more conditions (e.g. normal v cance...")
- 15:42, 4 May 2017 (diff | hist) . . (+1,013) . . Key Aspects of R Exercise
- 15:22, 4 May 2017 (diff | hist) . . (0) . . m Key Aspects of R Exercise (Rf moved page Key Aspects of R to Key Aspects of R Exercise)
- 15:22, 4 May 2017 (diff | hist) . . (+39) . . N Key Aspects of R (Rf moved page Key Aspects of R to Key Aspects of R Exercise) (current)
- 15:22, 4 May 2017 (diff | hist) . . (0) . . m Key Aspects of R Exercise (Rf moved page I2rda karx to Key Aspects of R)
- 15:22, 4 May 2017 (diff | hist) . . (+30) . . N I2rda karx (Rf moved page I2rda karx to Key Aspects of R) (current)
- 15:12, 4 May 2017 (diff | hist) . . (+551) . . Differential Expression Exercise
- 14:48, 4 May 2017 (diff | hist) . . (+521) . . Differential Expression Exercise
- 14:40, 4 May 2017 (diff | hist) . . (0) . . m Estimating Gene Count Exercise (Rf moved page I2rda egcx to Estimating Gene Count Exercise over redirect)
- 14:40, 4 May 2017 (diff | hist) . . (+44) . . N I2rda egcx (Rf moved page I2rda egcx to Estimating Gene Count Exercise over redirect) (current)
- 14:40, 4 May 2017 (diff | hist) . . (0) . . m Functional Analysis Exercise (Rf moved page I2rda fax to Functional Analysis Exercise over redirect)
- 14:40, 4 May 2017 (diff | hist) . . (+42) . . N I2rda fax (Rf moved page I2rda fax to Functional Analysis Exercise over redirect) (current)
- 14:24, 4 May 2017 (diff | hist) . . (+76) . . N Intro to RNA-Seq Data Analysis Course (Created page with "= Organizations Details = = Layout of the Day = = Access to the Machines =")
- 14:12, 4 May 2017 (diff | hist) . . (0) . . m Differential Expression Exercise (Rf moved page I2rda dex to Differential Expression Exercise over redirect)
- 14:12, 4 May 2017 (diff | hist) . . (+46) . . N I2rda dex (Rf moved page I2rda dex to Differential Expression Exercise over redirect) (current)
- 14:00, 4 May 2017 (diff | hist) . . (0) . . m Quality Control and Preprocessing Exercise (Rf moved page Quality Control and Processing Exercise to Quality Control and Preprocessing Exercise)
- 14:00, 4 May 2017 (diff | hist) . . (+56) . . N Quality Control and Processing Exercise (Rf moved page Quality Control and Processing Exercise to Quality Control and Preprocessing Exercise) (current)
- 13:59, 4 May 2017 (diff | hist) . . (0) . . m Quality Control and Preprocessing Exercise (Rf moved page Quality Control and Processing Talk to Quality Control and Processing Exercise)
- 13:59, 4 May 2017 (diff | hist) . . (+53) . . N Quality Control and Processing Talk (Rf moved page Quality Control and Processing Talk to Quality Control and Processing Exercise) (current)
- 13:58, 4 May 2017 (diff | hist) . . (0) . . m Quality Control and Preprocessing Exercise (Rf moved page Qcpx to Quality Control and Processing Talk)
- 13:58, 4 May 2017 (diff | hist) . . (+49) . . N Qcpx (Rf moved page Qcpx to Quality Control and Processing Talk) (current)
- 13:56, 4 May 2017 (diff | hist) . . (0) . . m Functional Analysis Exercise (Rf moved page Functional Analysis Exercise to I2rda fax)
- 13:55, 4 May 2017 (diff | hist) . . (0) . . m Differential Expression Exercise (Rf moved page Differential Expression Exercise to I2rda dex)
- 13:54, 4 May 2017 (diff | hist) . . (0) . . m Estimating Gene Count Exercise (Rf moved page Estimating Gene Count Exercise to I2rda egcx)
- 13:53, 4 May 2017 (diff | hist) . . (0) . . m Quality Control and Preprocessing Exercise (Rf moved page Quality Control and Preprocessing to Qcpx)
- 13:53, 4 May 2017 (diff | hist) . . (+18) . . N Quality Control and Preprocessing (Rf moved page Quality Control and Preprocessing to Qcpx) (current)
- 13:52, 4 May 2017 (diff | hist) . . (0) . . m I2rda m2rx (Rf moved page Mapping to Reference to I2rda m2rx) (current)
- 13:52, 4 May 2017 (diff | hist) . . (+24) . . N Mapping to Reference (Rf moved page Mapping to Reference to I2rda m2rx)
- 13:52, 4 May 2017 (diff | hist) . . (0) . . m Quality of Mapping Exercise (Rf moved page Mapping Quality Exercise to I2rda mqx)
- 13:52, 4 May 2017 (diff | hist) . . (+23) . . N Mapping Quality Exercise (Rf moved page Mapping Quality Exercise to I2rda mqx) (current)
- 13:51, 4 May 2017 (diff | hist) . . (0) . . m Key Aspects of R Exercise (Rf moved page Key Aspects of using R to I2rda karx)
- 13:51, 4 May 2017 (diff | hist) . . (+24) . . N Key Aspects of using R (Rf moved page Key Aspects of using R to I2rda karx) (current)
- 13:13, 2 May 2017 (diff | hist) . . (+4) . . I2rdalinks (current)
- 13:11, 2 May 2017 (diff | hist) . . (+453) . . N I2rdalinks (Created page with "= Introduction = One day is a very short time to deal with such a big topic as RNA-Seq Data Analysis, so this is page of links which attendees can view later in order to supp...")
- 17:51, 28 April 2017 (diff | hist) . . (+2,440) . . Samtools
- 00:07, 28 April 2017 (diff | hist) . . (+103) . . Qualimap (current)
- 00:01, 28 April 2017 (diff | hist) . . (+937) . . Qualimap
- 15:40, 26 April 2017 (diff | hist) . . (+185) . . Qualimap
- 15:36, 26 April 2017 (diff | hist) . . (+234) . . N Qualimap (Created page with "= Introduction = Inspecting bam files for quality = Installation = Has a number of dependencies: * optparse (available from CRAN) * NOISeq, Repitools, Rsamtools, GenomicFe...")
- 15:09, 26 April 2017 (diff | hist) . . (+217) . . Samtools
- 12:00, 26 April 2017 (diff | hist) . . (+16) . . Main Page
- 23:38, 19 April 2017 (diff | hist) . . (+966) . . N Hdi2u S25 (Created page with "= Accessing a running program or working with others interactively = * If you just run a job and then close down the terminal you ran it from, normally the job will be termin...") (current)
- 23:38, 19 April 2017 (diff | hist) . . (+538) . . N Hdi2u S24 (Created page with "= Processes = * Sometimes a command or program you run in the terminal goes on too long, or is obviously doing something you did not plan. * If there is no obvious way (such...") (current)
- 23:38, 19 April 2017 (diff | hist) . . (+385) . . N Hdi2u S23 (Created page with "= Environment Variables = * We have seen that the way commands run can be modified by the options passed on the command line. * One of the most important variables is PATH. T...") (current)
- 23:37, 19 April 2017 (diff | hist) . . (+793) . . N Hdi2u S22 (Created page with "* Try the command: grep "^DE" hsy14768.embl and grep -x "DE.*" hsy14768.embl * What are the <code>^</code> symbol and the <code>-x</code> parameter in these commands doing? *...") (current)
- 23:37, 19 April 2017 (diff | hist) . . (+830) . . N Hdi2u S21 (Created page with "= Grep = * grep stands for "global regular expression print" * you use this command to search for text patterns in a file, for example, Linux's mini-dicitonary. grep "adge"...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+262) . . N Hdi2u S20 (Created page with "= Piping output between applications = * <code>|</code>, often called an operator because it's so powerful * not always easy to find on the keyboard == Exercise == * "Pipe" t...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+1,235) . . N Hdi2u S19 (Created page with "= Removing files and directories = * The key difference between deleting something from the command line and using the graphical file browser is that in the first case the fi...") (current)
- 23:36, 19 April 2017 (diff | hist) . . (+352) . . N Hdi2u S18 (Created page with "= Linking to files = * copying big files can exhaust hard disk quickly. * You can instead create a link to it with the <code>ln -s</code> command. ln -s current.file linktoc...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,381) . . N Hdi2u S17 (Created page with "= Copying files and directories = * The basic command used to copy files using the command line is <code>cp</code>. * At a minimum, you must specify two arguments: the name o...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,425) . . N Hdi2u S16 (Created page with "== Getting by in only normal mode == * movement keys, "w" jump via start of words; "e" jump via ends; "fc" jump to next c * "0" for start of line, "A" for end of line and int...") (current)
- 23:35, 19 April 2017 (diff | hist) . . (+1,203) . . N Hdi2u S15 (Created page with "= Text editing = * There are very many text editors, but one of the most powerful and dependable is <code>vi</code>. * It has a steep but tiny learning curve, which we hope t...") (current)
- 23:34, 19 April 2017 (diff | hist) . . (+648) . . N Hdi2u S14 (Created page with "== Remember the man pages == There are many command line options available for each of the above commands, as well as functionality we do not cover here. To read more about th...") (current)
- 23:34, 19 April 2017 (diff | hist) . . (+1,212) . . N Hdi2u S13 (Created page with "= Reading text files = * These are useful when you want to look at the contents of a file, but not edit it. * Among the most common of these commands are <code>cat</code>, <c...") (current)
- 23:33, 19 April 2017 (diff | hist) . . (+1,249) . . N Hdi2u S12 (Created page with "= Command history = * This is another very handy tool for saving typing * Previous commands you have used are stored in your "history". * You use the up and down arrow keys t...") (current)
- 23:32, 19 April 2017 (diff | hist) . . (+1,265) . . N Hdi2u S11 (Created page with "= Tab completion = * Fear of the command line often means, fear of typing too much. Everybody fears this, so there are tools. * Tab completion is probably the most important...") (current)
- 23:32, 19 April 2017 (diff | hist) . . (+1,271) . . N Hdi2u S10 (Created page with "= Changing directories = * Directories are the same as folders. In linux "directory" is more common. * Directories within directories are called subdirectories" * The command...") (current)
- 23:31, 19 April 2017 (diff | hist) . . (+908) . . N Hdi2u S09 (Created page with "= Linux shortcut symbols = * We've seen <code>*</code> is a special symbol, and how useful it can be. * There are more however: * <code>?</code> matches a single character l...") (current)
- 23:30, 19 April 2017 (diff | hist) . . (+765) . . N Hdi2u S08 (Created page with "= Basic Linux tips for filenames = * Linux does not deal well with spaces in filenames * Expect problems when transferring files from Windows. * Everything is case sensitive...") (current)
- 23:30, 19 April 2017 (diff | hist) . . (+440) . . N Hdi2u S07 (Created page with "Now try: man ls * Did you think you knew this command already? * What does the <code>-h</code> option do? What about the <code>-a</code> option? What would running <code>ls...") (current)
- 23:29, 19 April 2017 (diff | hist) . . (+42) . . Hdi2u S06 (current)
- 23:28, 19 April 2017 (diff | hist) . . (+854) . . N Hdi2u S06 (Created page with "= Learning about Linux commands = * This is a continuous and very important activity * Linux has a large and comprehensive documentation system called <code>man</code> * Linu...")
- 23:28, 19 April 2017 (diff | hist) . . (+883) . . N Hdi2u S05 (Created page with "== Answers == * You get the hidden files * the <code>-l</code> is the long listing * this file is empty, it has no content. * by default ls will list files anywhere it can fi...") (current)
- 23:27, 19 April 2017 (diff | hist) . . (+972) . . N Hdi2u S04 (Created page with "= Listing files and directories = * <code>ls</code> is the most common command of all. It lists files and folders in your current location. * By default it requires no argume...") (current)
- 23:27, 19 April 2017 (diff | hist) . . (+928) . . N Hdi2u S03 (Created page with "= Navigating the command line = * Bioinformatics tools can have very many options * They also can be combined with many others, leading to very long command-line. * You do no...") (current)
- 23:26, 19 April 2017 (diff | hist) . . (+1,096) . . N Hdi2u S02 (Created page with "= Anatomy of a Command = <command> <options/parameters> <arguments> * <command> what do I want to do? * <options/parameters> how do I want to do it? * <arguments>, on what...") (current)
- 23:26, 19 April 2017 (diff | hist) . . (-1,098) . . Hdi2u S01 (current)
- 23:25, 19 April 2017 (diff | hist) . . (-22,344) . . Hdi2u S01
- 23:25, 19 April 2017 (diff | hist) . . (+24,146) . . N Hdi2u S01 (Created page with "= The Command-line (shell) = The real power of Linux/Unix systems is the command line. * Many programs and facilities are available through graphical options on Linux, but a...")
- 23:24, 19 April 2017 (diff | hist) . . (+24,146) . . N Hdi2u S00 (n) (current)
- 22:47, 19 April 2017 (diff | hist) . . (+2,967) . . N Hdi2u intro (Created page with "= Course schedule = * This is a cut-down version of 1 day course. * History and theory has been left out * Scripting is excluded (although plenty of one-liners) * Maximise pr...") (current)
- 17:34, 19 April 2017 (diff | hist) . . (+3,839) . . N Hdi2u dirorg exercise (n) (current)
- 14:45, 19 April 2017 (diff | hist) . . (+1,497) . . Hdi2u rendertotsv exercise (current)
- 14:37, 19 April 2017 (diff | hist) . . (+4,589) . . N Hdi2u rendertotsv exercise (n)
- 14:34, 19 April 2017 (diff | hist) . . (-1,969) . . Hdi2u commandbased exercises (current)
- 14:30, 19 April 2017 (diff | hist) . . (+26,115) . . N Hdi2u commandbased exercises (Created page with "= The Command-line (shell) = The real power of Linux/Unix systems is the command line. * Many programs and facilities are available through graphical options on Linux, but a...")
- 14:29, 19 April 2017 (diff | hist) . . (+30) . . Main Page
- 22:02, 17 April 2017 (diff | hist) . . (+321) . . One-liners (current)
- 21:42, 17 April 2017 (diff | hist) . . (+250) . . One-liners
- 00:09, 15 April 2017 (diff | hist) . . (-2,136) . . Biolinux Source course (current)
- 23:55, 14 April 2017 (diff | hist) . . (-9,484) . . Biolinux Source course
- 18:53, 14 April 2017 (diff | hist) . . (-601,958) . . Biolinux Source course
- 18:51, 14 April 2017 (diff | hist) . . (+430) . . Course itself (current)
- 17:21, 14 April 2017 (diff | hist) . . (0) . . Main Page
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