User contributions
- 10:52, 25 February 2015 (diff | hist) . . (+38) . . Photo (→2014 Workshop) (current)
- 10:49, 25 February 2015 (diff | hist) . . (0) . . N File:XenBioinfo 2014b.jpg (current)
- 10:47, 25 February 2015 (diff | hist) . . (+139) . . Photo (→2014 Workshop)
- 10:45, 25 February 2015 (diff | hist) . . (+6) . . Photo (→2014 Workshop)
- 10:44, 25 February 2015 (diff | hist) . . (+49) . . N Photo (Created page with "== 2014 Workshop == Image:XenBioinfo_2014.jpg")
- 10:44, 25 February 2015 (diff | hist) . . (+15) . . MediaWiki:Sidebar (current)
- 10:43, 25 February 2015 (diff | hist) . . (+31) . . Main Page (current)
- 10:42, 25 February 2015 (diff | hist) . . (0) . . N File:XenBioinfo 2014.jpg (current)
- 13:26, 12 January 2015 (diff | hist) . . (+232) . . RSEM (current)
- 13:10, 12 January 2015 (diff | hist) . . (+298) . . RSEM
- 18:15, 11 January 2015 (diff | hist) . . (+133) . . N RSEM (Created page with "== Prepare reference sequences == $ rsem-prepare-reference my_fasta.fa my_fasta.rsem == Convert SAM file == ---- Category:HowTo")
- 11:06, 2 December 2014 (diff | hist) . . (+1,310) . . N GeneIdentifier (Created page with "= JGI annotation for ''Xenopus laevis'' = == From XenBase FTP == * Xenla6.0 (ftp://ftp.xenbase.org/pub/Genomics/JGI/Xenla6.0/) XeXenL6RMv10+numeric_id+'m' (e.g. XeXenL6RMv10...") (current)
- 14:39, 17 November 2014 (diff | hist) . . (+233) . . STAR (current)
- 16:17, 22 October 2014 (diff | hist) . . (+430) . . BWA (current)
- 13:33, 22 October 2014 (diff | hist) . . (+126) . . STAR (→Build a database)
- 00:22, 22 October 2014 (diff | hist) . . (+18) . . STAR (→Build a database)
- 00:21, 22 October 2014 (diff | hist) . . (+378) . . N STAR (Created page with "== Build a database == $ /path/to/star/STAR --runMode genomeGenerate --genomeDir <dir_name> \ --genomeFastaFiles <fasta_file> --runThread<N> == See also == * Project home ...")
- 15:08, 21 October 2014 (diff | hist) . . (+188) . . N GMAP (Created page with "== Build a database == $ /path/to/gmap/bin/gmap_buid -D dest_dir_name -d db_name seq.fasta == See also == * Project homepage - http://research-pub.gene.com/gmap/ ---- Cat...") (current)
- 15:04, 21 October 2014 (diff | hist) . . (+92) . . N BWA (Created page with " == See also == * Project website - http://bio-bwa.sourceforge.net/ ---- Category:HowTo")
- 10:28, 21 October 2014 (diff | hist) . . (+4) . . Bowtie1 (→Run it!) (current)
- 10:27, 21 October 2014 (diff | hist) . . (+1,845) . . N Bowtie1 (Created page with "== Installation == * Download pre-compiled program from the website below. ** Version 1.1.1 is available at http://sourceforge.net/projects/bowtie-bio/files/bowtie/1.1.1/ * Un...")
- 13:26, 17 May 2014 (diff | hist) . . (-61) . . List of sessions (→Day 7 - 5/17/2014) (current)
- 13:02, 17 May 2014 (diff | hist) . . (+179) . . BLAST+ HowTo (→Download & install the program) (current)
- 11:34, 17 May 2014 (diff | hist) . . (+48) . . List of sessions (→Day 7 - 5/17/2014)
- 11:32, 17 May 2014 (diff | hist) . . (+94) . . List of sessions (→Day 7 - 5/17/2014)
- 11:01, 17 May 2014 (diff | hist) . . (+25) . . N Functional Network (Created page with "http://www.cytoscape.org/") (current)
- 10:31, 17 May 2014 (diff | hist) . . (+10) . . Microarray (current)
- 10:30, 17 May 2014 (diff | hist) . . (+3,304) . . N Microarray (Created page with "* http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE12613 = exp.txt = <pre> Filename Sample Group Description CEL/GSM315919.CEL ICD1 ICD ICD-1 CEL/G...")
- 06:13, 17 May 2014 (diff | hist) . . (0) . . List of sessions (→Day 7 - 5/17/2014)
- 06:13, 17 May 2014 (diff | hist) . . (+319) . . N Orthology (Created page with "= Databases = * InParanoid - http://inparanoid.sbc.su.se/cgi-bin/index.cgi * OrthoMCL - http://orthomcl.org/orthomcl/ * TreeFam - http://www.treefam.org/ (only animal) * EggN...") (current)
- 06:07, 17 May 2014 (diff | hist) . . (+339) . . N HowTo MeV (Created page with "[http://www.tm4.org/mev.html MeV]('MultiExperiment Viewer') is a viewer in TM4 package (microarray software suite). Although it is designed for microarray, all analysis functi...") (current)
- 05:57, 17 May 2014 (diff | hist) . . (+105) . . List of sessions (→Day 7 - 5/17/2014)
- 00:52, 17 May 2014 (diff | hist) . . (-2) . . List of sessions (→Day 6 - 5/16/2014)
- 00:51, 17 May 2014 (diff | hist) . . (0) . . m SNP analysis (TaejoonKwon moved page SNP and Galaxy to SNP analysis: Moved galaxy to other session) (current)
- 00:51, 17 May 2014 (diff | hist) . . (+26) . . N SNP and Galaxy (TaejoonKwon moved page SNP and Galaxy to SNP analysis: Moved galaxy to other session) (current)
- 14:49, 16 May 2014 (diff | hist) . . (+73) . . List of sessions (→Day 6 - 5/16/2014)
- 14:34, 16 May 2014 (diff | hist) . . (+292) . . List of sessions (→Day 6 - 5/16/2014)
- 14:33, 16 May 2014 (diff | hist) . . (-44) . . List of sessions (→Day 6 - 5/16/2014)
- 14:31, 16 May 2014 (diff | hist) . . (+117) . . List of sessions (→Day 5 - 5/15/2014)
- 14:28, 16 May 2014 (diff | hist) . . (+14) . . ChIPseq motif (current)
- 14:27, 16 May 2014 (diff | hist) . . (+238) . . ChIPseq motif
- 14:24, 16 May 2014 (diff | hist) . . (+196) . . ChIPseq motif
- 14:23, 16 May 2014 (diff | hist) . . (+10,558) . . N ChIPseq motif (Created page with "You took fastq reads from an H3K4me3 experiment, made a genomic bowtie2 index from a fasta file, aligned the reads, converted the aligned sam files to bam files, sorted them, ...")
- 14:19, 16 May 2014 (diff | hist) . . (+26) . . List of sessions (→Day 6 - 5/16/2014)
- 08:29, 16 May 2014 (diff | hist) . . (+137) . . List of sessions (→References)
- 18:58, 15 May 2014 (diff | hist) . . (-16) . . SNP analysis (→How to find SNPs)
- 18:56, 15 May 2014 (diff | hist) . . (+3,147) . . N SNP analysis (Created page with "= How to find SNPs = mpileup file: <pre> TranscriptID position base@position actual_reads_and_qual E2F4|ENSG00000205250|c.XGI_TC419474|JGIv7b.000015416_1879975-19...")
- 18:50, 15 May 2014 (diff | hist) . . (+32) . . List of sessions (→Day 6 - 5/16/2014)
- 18:50, 15 May 2014 (diff | hist) . . (-6) . . List of sessions (→Day 5 - 5/15/2014)
- 18:49, 15 May 2014 (diff | hist) . . (-14) . . Main Page (→Course)
- 14:10, 15 May 2014 (diff | hist) . . (+4) . . ChIPseq prep and map (→IGV)
- 13:51, 15 May 2014 (diff | hist) . . (-2) . . ChIPseq prep and map (→Mapping)
- 13:43, 15 May 2014 (diff | hist) . . (-6) . . ChIPseq prep and map
- 13:02, 15 May 2014 (diff | hist) . . (+3) . . ChIPseq prep and map
- 13:01, 15 May 2014 (diff | hist) . . (+2,554) . . N Machine Learning with MATLAB (Created page with "<syntaxhighlight lang="matlab"> %import our Definitions File. This file contains accession numbers, genes symbols and other information Defs = importdata('Defs.txt'); %impor...") (current)
- 13:00, 15 May 2014 (diff | hist) . . (+2) . . List of sessions (→Day 5 - 5/15/2014)
- 11:32, 15 May 2014 (diff | hist) . . (-1) . . Main Page (→Resources)
- 11:30, 15 May 2014 (diff | hist) . . (+889) . . ChIPseq prep and map
- 11:17, 15 May 2014 (diff | hist) . . (+364) . . ChIPseq prep and map
- 11:01, 15 May 2014 (diff | hist) . . (+12,385) . . N ChIPseq prep and map (Created page with "Moving forward, when I want you to do commands, I will indent the command and precede it with “$”. When you cut and paste the command, don’t include that sign. It will l...")
- 10:42, 15 May 2014 (diff | hist) . . (+148) . . List of sessions (→Day 3 - 5/13/2014)
- 10:40, 15 May 2014 (diff | hist) . . (+255) . . List of sessions (→Day 5 - 5/15/2014)
- 10:37, 15 May 2014 (diff | hist) . . (+142) . . List of sessions (→Day 5 - 5/15/2014)
- 15:31, 14 May 2014 (diff | hist) . . (+65) . . List of sessions (→Day 4 - 5/14/2014)
- 15:30, 14 May 2014 (diff | hist) . . (-113) . . List of sessions (→Day 4 - 5/14/2014)
- 09:53, 14 May 2014 (diff | hist) . . (+150) . . List of sessions (→Day 3 - 5/13/2014)
- 09:00, 13 May 2014 (diff | hist) . . (+265) . . N RNAseq part1 (Created page with "= Flowchart = # Enrichment: poly-A or Ribosome depletion # Fragmentation # Amplification # Repair # Amplification # A's # Amplification # Ligation # Amplifcation = See also =...") (current)
- 08:54, 13 May 2014 (diff | hist) . . (+255) . . List of sessions (→References)
- 08:44, 13 May 2014 (diff | hist) . . (+5) . . List of sessions (→Day 3 - 5/13/2014)
- 08:43, 13 May 2014 (diff | hist) . . (+65) . . List of sessions (→Day 3 - 5/13/2014)
- 16:57, 12 May 2014 (diff | hist) . . (+74) . . Awk (current)
- 16:50, 12 May 2014 (diff | hist) . . (+74) . . List of sessions (→Day 2 - 5/12/2014)
- 14:14, 12 May 2014 (diff | hist) . . (+101) . . Intro to Programming and Python (→Python) (current)
- 10:37, 12 May 2014 (diff | hist) . . (+79) . . Main Page
- 10:20, 12 May 2014 (diff | hist) . . (+3) . . List of sessions
- 10:16, 12 May 2014 (diff | hist) . . (+155) . . N Awk (Created page with "* http://data.marcottelab.org/XenBioinfo2014/pdf/awk_LP.pdf -- Lecture Note * http://data.marcottelab.org/XenBioinfo2014/pdf/awk_cheatsheet_LP.pdf -- Cheat")
- 09:39, 12 May 2014 (diff | hist) . . (+93) . . Main Page (→Resources)
- 09:37, 12 May 2014 (diff | hist) . . (+107) . . List of sessions
- 08:26, 12 May 2014 (diff | hist) . . (-70) . . List of sessions (→Day 2 - 5/12/2014)
- 16:09, 8 May 2014 (diff | hist) . . (+57) . . Github HowTo (current)
- 14:29, 8 May 2014 (diff | hist) . . (-5) . . List of participants 2014 (current)
- 16:08, 7 May 2014 (diff | hist) . . (+12) . . List of participants 2014
- 11:28, 7 May 2014 (diff | hist) . . (+57) . . List of participants 2014
- 15:21, 6 May 2014 (diff | hist) . . (+16) . . List of participants 2014
- 14:49, 6 May 2014 (diff | hist) . . (+11) . . List of participants 2014 (→Mac OSX)
- 14:49, 6 May 2014 (diff | hist) . . (0) . . List of participants 2014
- 14:47, 6 May 2014 (diff | hist) . . (0) . . List of participants 2014
- 14:46, 6 May 2014 (diff | hist) . . (-12) . . List of participants 2014 (→Mac OSX)
- 14:46, 6 May 2014 (diff | hist) . . (+50) . . List of participants 2014
- 13:49, 6 May 2014 (diff | hist) . . (+56) . . List of participants 2014
- 13:44, 6 May 2014 (diff | hist) . . (-8) . . List of participants 2014
- 12:55, 5 May 2014 (diff | hist) . . (+189) . . List of programs (→Basic tools) (current)
- 12:53, 5 May 2014 (diff | hist) . . (+145) . . Intro to Programming and Python (→Python)
- 10:08, 2 May 2014 (diff | hist) . . (+183) . . List of participants 2014
- 19:00, 1 May 2014 (diff | hist) . . (+448) . . Shotgun Proteomics Data Process (→See also) (current)
- 17:20, 1 May 2014 (diff | hist) . . (+117) . . N Shotgun Proteomics Data Process (Created page with " = See also = * http://proteome-software.wikispaces.com/Proteomics (Documents from Proteome Software/Brian Searl) **")
- 17:12, 1 May 2014 (diff | hist) . . (+66) . . List of sessions (→Day 3 - 5/13/2014)
- 16:53, 1 May 2014 (diff | hist) . . (+3) . . List of sessions (→Day 4 - 5/14/2014)
- 16:04, 1 May 2014 (diff | hist) . . (+86) . . Shotgun Proteomics Theory (→See also) (current)
- 16:02, 1 May 2014 (diff | hist) . . (+314) . . N Shotgun Proteomics Theory (Created page with " = See also = * Thermo Orbitrap Elite - https://www.youtube.com/watch?v=KjUQYuy3msA * Thermo Q-Exactive - https://www.youtube.com/watch?v=fqfyyravJkA * Brief Intro to Mass Spe...")
- 15:58, 1 May 2014 (diff | hist) . . (+162) . . List of sessions (→Day 4 - 5/14/2014)
- 12:52, 1 May 2014 (diff | hist) . . (0) . . List of participants 2014
- 12:48, 1 May 2014 (diff | hist) . . (+986) . . N Point of significance (Created page with "= List = * Nonparametric tests (May 2014) - http://www.nature.com/nmeth/journal/v11/n5/full/nmeth.2937.html * Comparing samples, Part 2 (Apr 2014) - http://www.nature.com/nmet...") (current)
- 12:39, 1 May 2014 (diff | hist) . . (+68) . . Main Page (→Resources)
- 12:17, 1 May 2014 (diff | hist) . . (+167) . . List of participants 2014
- 22:22, 30 April 2014 (diff | hist) . . (+17) . . List of participants 2014
- 21:21, 30 April 2014 (diff | hist) . . (+34) . . List of participants 2014
- 12:33, 30 April 2014 (diff | hist) . . (+23) . . List of participants 2014
- 11:56, 30 April 2014 (diff | hist) . . (+33) . . List of participants 2014 (→Joined (Google Group))
- 11:54, 30 April 2014 (diff | hist) . . (+19) . . List of participants 2014 (→Joined (Google Group))
- 11:50, 30 April 2014 (diff | hist) . . (0) . . List of participants 2014
- 11:26, 28 April 2014 (diff | hist) . . (+899) . . Intro to Programming and Python (→Other high-level 'scripting' languages)
- 11:15, 28 April 2014 (diff | hist) . . (+276) . . Intro to Programming and Python (→See also)
- 11:11, 28 April 2014 (diff | hist) . . (+315) . . Intro to Programming and Python
- 11:05, 28 April 2014 (diff | hist) . . (+762) . . N Intro to Programming and Python (Created page with " = Other high-level 'scripting' languages = == Perl == * http://www.bioperl.org/wiki/How_Perl_saved_human_genome ("How PERL saved human genome" by Lincoln D. Stein) * http://w...")
- 10:52, 28 April 2014 (diff | hist) . . (+29) . . MediaWiki:Sidebar
- 10:51, 28 April 2014 (diff | hist) . . (-2) . . m List of participants 2014 (→Joined (Google Group) =)
- 10:50, 28 April 2014 (diff | hist) . . (+634) . . N List of participants 2014 (Created page with "= Joined (Google Group) == https://groups.google.com/forum/#!forum/xenopus-bioinfo2014 * Sally Moody(samoody at gwu dot edu) * Asako Shindo (shindo at austin dot utexas dot e...")
- 17:05, 23 April 2014 (diff | hist) . . (+271) . . N Github HowTo (Created page with "= See also = * https://help.github.com/articles/set-up-git (How to set up git - from github.com) * https://help.github.com/articles/what-are-other-good-resources-for-learning-...")
- 17:01, 23 April 2014 (diff | hist) . . (+78) . . List of programs (→Basic sequence analysis)
- 17:00, 23 April 2014 (diff | hist) . . (+130) . . List of programs (→Programs used in the server side mostly)
- 16:58, 23 April 2014 (diff | hist) . . (-2) . . BLAST+ HowTo (→See also)
- 16:58, 23 April 2014 (diff | hist) . . (+208) . . List of programs (→Shotgun Proteomics data analysis)
- 16:55, 23 April 2014 (diff | hist) . . (+134) . . List of programs (→Data visualization analysis)
- 16:50, 23 April 2014 (diff | hist) . . (+60) . . Main Page (→Resources)
- 16:44, 23 April 2014 (diff | hist) . . (+40) . . List of programs (→Programming)
- 16:42, 23 April 2014 (diff | hist) . . (+221) . . List of programs (→Programs used in the server side mostly)
- 21:42, 17 April 2014 (diff | hist) . . (+29) . . List of databases (→Protein domains) (current)
- 21:42, 17 April 2014 (diff | hist) . . (+147) . . List of databases (→Protein domains)
- 21:40, 17 April 2014 (diff | hist) . . (+74) . . List of databases (→Genome in general (including ENCODE))
- 21:39, 17 April 2014 (diff | hist) . . (+51) . . List of databases (→Process/Pathway/Network)
- 21:39, 17 April 2014 (diff | hist) . . (+29) . . List of databases (→Other model organism)
- 21:38, 17 April 2014 (diff | hist) . . (+86) . . List of databases (→Gene expression)
- 21:37, 17 April 2014 (diff | hist) . . (-8) . . List of databases (→Orthology)
- 21:36, 17 April 2014 (diff | hist) . . (+131) . . List of databases (→Orthology)
- 21:35, 17 April 2014 (diff | hist) . . (+155) . . List of databases (→Genome in general (including ENCODE))
- 21:32, 17 April 2014 (diff | hist) . . (+552) . . N List of databases (Created page with "= Xenopus = * http://www.xenbase.org/entry/ * http://genomics.nimr.mrc.ac.uk/cgi-bin/search.exe - ''Xenopus'' Image Annotator (a.k.a. GenMARK) * http://xenopus.nibb.ac.jp/ (NI...")
- 20:57, 17 April 2014 (diff | hist) . . (+24) . . Main Page (→Resources)
- 20:56, 17 April 2014 (diff | hist) . . (+82) . . BLAST+ HowTo
- 15:37, 17 April 2014 (diff | hist) . . (+5) . . BLAST+ HowTo (→Run the search)
- 15:36, 17 April 2014 (diff | hist) . . (0) . . m BLAST+ HowTo (TaejoonKwon moved page HowTo BLAST+ to BLAST+ HowTo: Consistency)
- 15:36, 17 April 2014 (diff | hist) . . (+26) . . N HowTo BLAST+ (TaejoonKwon moved page HowTo BLAST+ to BLAST+ HowTo: Consistency) (current)
- 15:36, 17 April 2014 (diff | hist) . . (+48) . . BLAST HowTo (current)
- 15:35, 17 April 2014 (diff | hist) . . (0) . . m BLAST HowTo (TaejoonKwon moved page HowTo BLAST to BLAST HowTo: Consistency)
- 15:35, 17 April 2014 (diff | hist) . . (+25) . . N HowTo BLAST (TaejoonKwon moved page HowTo BLAST to BLAST HowTo: Consistency) (current)
- 15:34, 17 April 2014 (diff | hist) . . (+338) . . BLAST+ HowTo (→Download program)
- 15:31, 17 April 2014 (diff | hist) . . (+88) . . BLAST HowTo
- 15:29, 17 April 2014 (diff | hist) . . (+716) . . N BLAST+ HowTo (Created page with "= Download program = * ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ** Old version: ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/ = Make sequence databa...")
- 15:13, 17 April 2014 (diff | hist) . . (+69) . . BLAST HowTo (→Download)
- 15:12, 17 April 2014 (diff | hist) . . (+99) . . N BLAST HowTo (Created page with "= Download = * ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ ---- Category:HowTo")
- 15:11, 17 April 2014 (diff | hist) . . (+37) . . N Category:HowTo (Created page with "Collection of 'How To ...' documents.") (current)
- 15:10, 17 April 2014 (diff | hist) . . (0) . . MediaWiki:Sidebar
- 15:09, 17 April 2014 (diff | hist) . . (+24) . . Main Page
- 12:49, 17 April 2014 (diff | hist) . . (+24) . . List of sessions (→Day 3 - 5/13/2014)
- 12:49, 17 April 2014 (diff | hist) . . (+932) . . N List of sessions (Created page with "= Day 2 - 5/12/2014 = * Intro_to_Unix_and_Scripting (Leon) * Intro_to_Programming_and_Python (Taejoon) * Xenopus_genome (Taejoon) * Xenopus_DevStage_expression_...")
- 12:22, 17 April 2014 (diff | hist) . . (0) . . Main Page (→Instructors)
- 11:44, 17 April 2014 (diff | hist) . . (0) . . Main Page
- 11:44, 17 April 2014 (diff | hist) . . (+197) . . Main Page
- 11:42, 17 April 2014 (diff | hist) . . (+75) . . Main Page (→Course)
- 11:41, 17 April 2014 (diff | hist) . . (+83) . . N LSF HowTo (Created page with "* https://wiki.med.harvard.edu/Orchestra/IntroductionToLSF ---- Category:HowTo") (current)
- 11:41, 17 April 2014 (diff | hist) . . (+248) . . Main Page (→Course)
- 11:38, 17 April 2014 (diff | hist) . . (+116) . . Main Page (→Instructors)
- 11:27, 17 April 2014 (diff | hist) . . (0) . . Main Page (→Course)
- 11:26, 17 April 2014 (diff | hist) . . (+153) . . N MediaWiki:Sidebar (Created page with " * navigation ** mainpage|mainpage-description ** recentchanges-url|recentchanges ** Category:Howto|HowTo ** helppage|help * SEARCH * TOOLBOX * LANGUAGES")
- 11:25, 17 April 2014 (diff | hist) . . (+489) . . List of programs
- 11:20, 17 April 2014 (diff | hist) . . (+147) . . List of programs (→Programming)
- 11:18, 17 April 2014 (diff | hist) . . (+430) . . List of programs
- 11:13, 17 April 2014 (diff | hist) . . (+848) . . N List of programs (Created page with "= Basic tools = * Terminal ** Mac and Linux: You already have it. Search 'Terminal'. ** Windows: [http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html PuTTY] may ...")
- 10:41, 17 April 2014 (diff | hist) . . (+14) . . Main Page (→Course)
- 10:40, 17 April 2014 (diff | hist) . . (+275) . . Main Page (→Resources)
- 10:32, 17 April 2014 (diff | hist) . . (+75) . . Main Page (→Instructors)
- 10:32, 17 April 2014 (diff | hist) . . (+122) . . Main Page
- 10:26, 17 April 2014 (diff | hist) . . (+262) . . Main Page
- 10:22, 17 April 2014 (diff | hist) . . (+215) . . Main Page
- 10:19, 17 April 2014 (diff | hist) . . (+19) . . Main Page
- 10:19, 17 April 2014 (diff | hist) . . (-289) . . Main Page