User contributions
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- 13:59, 24 January 2018 (diff | hist) . . (+1,232) . . RedHat
- 18:05, 5 December 2017 (diff | hist) . . (+22) . . Hardware Issues (current)
- 11:07, 1 December 2017 (diff | hist) . . (+879) . . N PairwiseCallSNPs (Created page with "= Introduction = The following pipeline evolved from the callSNPs.py script developed by Miguel Pinheiro, following collaboration with Souad Alateah and operating on her myco...") (current)
- 10:39, 1 December 2017 (diff | hist) . . (+23) . . Main Page
- 17:14, 30 November 2017 (diff | hist) . . (+275) . . RedHat
- 16:54, 24 November 2017 (diff | hist) . . (+226) . . PASA (current)
- 16:47, 24 November 2017 (diff | hist) . . (+654) . . PASA
- 16:40, 24 November 2017 (diff | hist) . . (+680) . . N PASA (Created page with "= Introduction = Brian Haas also behind this Splice Alignment tool. = Installation = * The PASA mysql user requires full privileges so it can create databases, which it app...")
- 16:26, 24 November 2017 (diff | hist) . . (+12) . . Main Page
- 17:16, 20 November 2017 (diff | hist) . . (+63) . . RedHat
- 17:03, 20 November 2017 (diff | hist) . . (+132) . . RedHat
- 16:57, 20 November 2017 (diff | hist) . . (0) . . RedHat
- 16:56, 20 November 2017 (diff | hist) . . (+101) . . RedHat
- 16:55, 20 November 2017 (diff | hist) . . (+3,482) . . RedHat
- 16:51, 20 November 2017 (diff | hist) . . (+214) . . RedHat
- 16:18, 20 November 2017 (diff | hist) . . (+89) . . RedHat
- 16:15, 20 November 2017 (diff | hist) . . (0) . . RedHat
- 16:15, 20 November 2017 (diff | hist) . . (+126) . . RedHat
- 16:10, 20 November 2017 (diff | hist) . . (+513) . . RedHat
- 15:35, 20 November 2017 (diff | hist) . . (-2) . . Node1 issues (current)
- 15:33, 20 November 2017 (diff | hist) . . (+17) . . Node1 issues
- 16:04, 17 November 2017 (diff | hist) . . (+175) . . Canu (current)
- 14:48, 9 November 2017 (diff | hist) . . (+96) . . BLAST (current)
- 16:49, 8 November 2017 (diff | hist) . . (+65) . . H: drive on cluster
- 16:47, 8 November 2017 (diff | hist) . . (+653) . . H: drive on cluster
- 16:17, 8 November 2017 (diff | hist) . . (+692) . . H: drive on cluster
- 11:53, 8 November 2017 (diff | hist) . . (+360) . . m ChIP-Seq Top2 in Yeast 07.11.2017
- 11:51, 8 November 2017 (diff | hist) . . (+8,329) . . N ChIP-Seq Top2 in Yeast 07.11.2017 (Created page with "= Introduction = Fourth set of ChIP-Seq samples from David @ Dundee. = Listing = Principle folder: '''071117HelderAmy''' Subfolder: 2017_11_01_19_Amy1_L001-ds.0b52f56e8cbc...")
- 11:44, 8 November 2017 (diff | hist) . . (+40) . . Main Page
- 16:13, 3 November 2017 (diff | hist) . . (+205) . . H: drive on cluster
- 13:43, 3 November 2017 (diff | hist) . . (+218) . . Normalization (current)
- 13:41, 3 November 2017 (diff | hist) . . (+597) . . N Normalization (Created page with "= Introduction = Normalisation can mean different things depending on the context, but can mostly be summarized by saying that, when undertaking comparisons, it is necessary...")
- 13:28, 3 November 2017 (diff | hist) . . (+20) . . Main Page
- 18:03, 2 November 2017 (diff | hist) . . (+143) . . Repeatmasker (current)
- 16:50, 2 November 2017 (diff | hist) . . (+51) . . Repeatmasker
- 16:45, 2 November 2017 (diff | hist) . . (+264) . . Repeatmasker
- 16:21, 2 November 2017 (diff | hist) . . (+2,630) . . Repeatmasker
- 16:08, 2 November 2017 (diff | hist) . . (+210) . . Repeatmasker
- 15:54, 2 November 2017 (diff | hist) . . (+60) . . Repeatmasker
- 15:21, 2 November 2017 (diff | hist) . . (+357) . . Repeatmasker
- 14:15, 2 November 2017 (diff | hist) . . (+4,980) . . Repeatmasker
- 14:49, 1 November 2017 (diff | hist) . . (+474) . . ChIP-Seq Top2 in Yeast
- 21:40, 30 October 2017 (diff | hist) . . (+166) . . H: drive on cluster
- 16:05, 22 October 2017 (diff | hist) . . (+8) . . VCF (current)
- 16:04, 22 October 2017 (diff | hist) . . (+197) . . VCF
- 13:05, 21 October 2017 (diff | hist) . . (+65) . . Nseg (current)
- 13:04, 21 October 2017 (diff | hist) . . (+292) . . N Nseg (Created page with "=Introduction = Coded in C and oldish utility software from NCBI. Information on this software is not easy to find. GACRC however, comes to the rescue: * Author / Distribut...")
- 12:59, 21 October 2017 (diff | hist) . . (+12) . . Main Page
- 13:48, 20 October 2017 (diff | hist) . . (+222) . . Repeatmodeler (current)
- 13:21, 20 October 2017 (diff | hist) . . (+271) . . Repeatmodeler
- 13:17, 20 October 2017 (diff | hist) . . (+552) . . Repeatmodeler
- 13:03, 20 October 2017 (diff | hist) . . (+353) . . Repeatmodeler
- 12:37, 20 October 2017 (diff | hist) . . (+3) . . Repeatmodeler
- 12:11, 20 October 2017 (diff | hist) . . (+597) . . Repeatmodeler
- 11:38, 20 October 2017 (diff | hist) . . (+1,964) . . Repeatmodeler
- 10:56, 20 October 2017 (diff | hist) . . (+294) . . Repeatmodeler
- 10:21, 20 October 2017 (diff | hist) . . (+57) . . Repeatmodeler
- 10:19, 20 October 2017 (diff | hist) . . (+540) . . Repeatmodeler
- 09:56, 20 October 2017 (diff | hist) . . (+122) . . Repeatmodeler
- 09:39, 20 October 2017 (diff | hist) . . (+193) . . N Repeatmodeler (Created page with "= Introdcuction = = Installation notes = nseg and nmerge (included in nseg) are quite old programs coded in C by NCBI. These were installed on all machines in /usr/local/bi...")
- 09:30, 20 October 2017 (diff | hist) . . (+21) . . Main Page
- 14:19, 17 October 2017 (diff | hist) . . (+242) . . Biotime machine
- 14:07, 17 October 2017 (diff | hist) . . (+426) . . Biotime machine
- 13:47, 17 October 2017 (diff | hist) . . (+469) . . Biotime machine
- 13:38, 17 October 2017 (diff | hist) . . (+145) . . Biotime machine
- 13:34, 17 October 2017 (diff | hist) . . (+203) . . Biotime machine
- 09:55, 17 October 2017 (diff | hist) . . (+106) . . MinION (Oxford Nanopore) (current)
- 10:45, 16 October 2017 (diff | hist) . . (+113) . . SCAN-pc laptop (current)
- 10:36, 16 October 2017 (diff | hist) . . (+168) . . SCAN-pc laptop
- 10:31, 16 October 2017 (diff | hist) . . (+430) . . SCAN-pc laptop
- 11:59, 11 October 2017 (diff | hist) . . (+87) . . Bisulfite Sequencing (current)
- 11:57, 11 October 2017 (diff | hist) . . (+166) . . N Bisulfite Sequencing (Created page with "= Introduction = Sequencing which causes unmethylated cytosine to be repaced by uracil. In this way, the methylation (which silences genes) pattern can be detected.")
- 11:54, 11 October 2017 (diff | hist) . . (-1) . . Main Page
- 11:54, 11 October 2017 (diff | hist) . . (+27) . . Main Page
- 22:10, 9 October 2017 (diff | hist) . . (-1) . . ChIP-Seq Top2 in Yeast
- 21:51, 9 October 2017 (diff | hist) . . (+301) . . ChIP-Seq Top2 in Yeast
- 21:31, 9 October 2017 (diff | hist) . . (+133) . . ChIP-Seq Top2 in Yeast
- 21:26, 9 October 2017 (diff | hist) . . (+264) . . ChIP-Seq Top2 in Yeast
- 16:39, 9 October 2017 (diff | hist) . . (+286) . . ChIP-Seq Top2 in Yeast
- 16:34, 9 October 2017 (diff | hist) . . (+414) . . ChIP-Seq Top2 in Yeast
- 16:19, 9 October 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 in Yeast
- 16:13, 9 October 2017 (diff | hist) . . (+332) . . ChIP-Seq Top2 in Yeast
- 15:49, 9 October 2017 (diff | hist) . . (+157) . . GenomeTools (current)
- 12:31, 9 October 2017 (diff | hist) . . (+552) . . GenomeTools
- 10:05, 9 October 2017 (diff | hist) . . (+143) . . GenomeTools
- 10:47, 6 October 2017 (diff | hist) . . (+1) . . Banjo (current)
- 09:27, 6 October 2017 (diff | hist) . . (+84) . . CallSNPs.py (current)
- 09:09, 6 October 2017 (diff | hist) . . (+172) . . CallSNPs.py
- 09:07, 6 October 2017 (diff | hist) . . (+250) . . Banjo
- 08:10, 6 October 2017 (diff | hist) . . (+149) . . MicroRNAs
- 16:36, 5 October 2017 (diff | hist) . . (+64) . . ViennaRNA (current)
- 16:35, 5 October 2017 (diff | hist) . . (+65) . . Squid (current)
- 16:26, 5 October 2017 (diff | hist) . . (+223) . . Squid
- 16:24, 5 October 2017 (diff | hist) . . (+1) . . BLAST
- 16:23, 5 October 2017 (diff | hist) . . (+1,031) . . BLAST
- 13:30, 5 October 2017 (diff | hist) . . (+348) . . N Squid (Created page with "= Introduction = In the wide world of software, squid is a proxy server used in high traffic websites, but this squid is Sean Eddy's utilites for general sequence reading. I...")
- 13:28, 5 October 2017 (diff | hist) . . (+13) . . Main Page
- 12:36, 5 October 2017 (diff | hist) . . (-1) . . Perl (current)
- 12:35, 5 October 2017 (diff | hist) . . (+461) . . Perl
- 12:09, 5 October 2017 (diff | hist) . . (+25) . . Perl
- 12:08, 5 October 2017 (diff | hist) . . (+398) . . Perl
- 11:19, 5 October 2017 (diff | hist) . . (+369) . . ViennaRNA
- 11:17, 5 October 2017 (diff | hist) . . (0) . . Perl
- 11:16, 5 October 2017 (diff | hist) . . (+94) . . Perl
- 11:08, 5 October 2017 (diff | hist) . . (+417) . . N Perl (Created page with "= Introduction = Quite a large software package for dealing with RNA and RNA structure = Installation = New versions of perl follow this configuraion before compiling sh...")
- 11:03, 5 October 2017 (diff | hist) . . (+210) . . N ViennaRNA (Created page with "= Introduction = Quite a large software package for dealing with RNA and RNA structure = Installation = ViennaRNA has a perl interface as well as a python interface for bot...")
- 10:53, 5 October 2017 (diff | hist) . . (+32) . . Main Page
- 13:26, 4 October 2017 (diff | hist) . . (+314) . . MicroRNAs
- 13:14, 4 October 2017 (diff | hist) . . (+203) . . N MicroRNAs (Created page with "= Introduction = = Relevant Papers = == "Predicting effective microRNA target sites in mammalian mRNAs" == By Agarwal et al eLife 2015 , link [https://www.ncbi.nlm.nih.gov/p...")
- 13:09, 4 October 2017 (diff | hist) . . (+16) . . Main Page
- 16:30, 3 October 2017 (diff | hist) . . (+79) . . Banjo
- 16:23, 3 October 2017 (diff | hist) . . (+588) . . N Banjo (Created page with "= Introduction = Banjo is Bayesian Network software with a very range of applicability in terms of data sets. It is coded in java and can be activiated on the cluster with...")
- 16:18, 3 October 2017 (diff | hist) . . (+13) . . Main Page
- 09:11, 2 October 2017 (diff | hist) . . (+2,473) . . N ChIP-Seq Top2 in Yeast 12.09.2017 (Created page with "= Introduction = September 2017 sequencing of a series of datasets listed below = Raw dataset listing = * 2017_09_12_24_INP-56915985 2017-09-12-24-INP_S24_L001_R1_001.fast...")
- 09:08, 2 October 2017 (diff | hist) . . (+40) . . Main Page
- 08:52, 29 September 2017 (diff | hist) . . (-4) . . IGSR/1000 Genomes (current)
- 08:51, 29 September 2017 (diff | hist) . . (+336) . . IGSR/1000 Genomes
- 08:48, 29 September 2017 (diff | hist) . . (+122) . . N IGSR/1000 Genomes (Created page with "= Introduction = IGSR, the Internation Genome Sample Resource provides ongoing support for the 1000 Genomes Project data.")
- 08:46, 29 September 2017 (diff | hist) . . (+24) . . Main Page
- 12:52, 21 September 2017 (diff | hist) . . (+215) . . Roary (current)
- 17:00, 20 September 2017 (diff | hist) . . (-2) . . SCAN-pc laptop
- 16:59, 20 September 2017 (diff | hist) . . (+46) . . SCAN-pc laptop
- 16:59, 20 September 2017 (diff | hist) . . (+184) . . SCAN-pc laptop
- 16:57, 20 September 2017 (diff | hist) . . (+300) . . Incorrect rebooting of marvin 19.09.2017 (current)
- 13:38, 20 September 2017 (diff | hist) . . (+288) . . Incorrect rebooting of marvin 19.09.2017
- 13:35, 20 September 2017 (diff | hist) . . (+1,418) . . N Incorrect rebooting of marvin 19.09.2017 (Created page with "= Introduction = Following a much delayed maintenance period for marvin, the latest published update from RedHat on the 10 Sept 2017 (i.e. kernel 2.6.32-696.10.2.el6.x86_64)...")
- 12:49, 20 September 2017 (diff | hist) . . (+47) . . Main Page
- 15:12, 19 September 2017 (diff | hist) . . (+1,006) . . N SCAN-pc laptop (Created page with "= Introduction = Bought by Janet Cox-Singh for use exclusively with Oxford Nanopore's MinION USB sequencing devices = Recent Behaviour (Sept 2017) = The laptop will light...")
- 13:45, 19 September 2017 (diff | hist) . . (+21) . . Main Page
- 14:45, 15 September 2017 (diff | hist) . . (+48) . . Unicycler (current)
- 14:15, 15 September 2017 (diff | hist) . . (+253) . . Unicycler
- 14:10, 15 September 2017 (diff | hist) . . (+334) . . N Unicycler (Created page with "= Introduction = Assembles microbial genomes, like other tools, but with the differences that it handle different types of short and long reads so that it can make hybrid ass...")
- 12:24, 15 September 2017 (diff | hist) . . (+17) . . Main Page
- 15:40, 14 September 2017 (diff | hist) . . (+175) . . General Command-line Tips (current)
- 09:52, 8 September 2017 (diff | hist) . . (+1) . . ChIP-Seq Top2 in Yeast
- 09:51, 8 September 2017 (diff | hist) . . (+336) . . ChIP-Seq Top2 in Yeast
- 17:05, 21 August 2017 (diff | hist) . . (+280) . . RedHat
- 16:55, 21 August 2017 (diff | hist) . . (+133) . . RedHat
- 16:53, 21 August 2017 (diff | hist) . . (+612) . . RedHat
- 22:43, 8 August 2017 (diff | hist) . . (+10) . . ChIP-Seq Top2 in Yeast
- 22:41, 8 August 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 in Yeast
- 22:29, 8 August 2017 (diff | hist) . . (+1,164) . . ChIP-Seq Top2 in Yeast
- 10:34, 8 August 2017 (diff | hist) . . (-12) . . ChIP-Seq Top2 in Yeast
- 10:31, 8 August 2017 (diff | hist) . . (+1,449) . . ChIP-Seq Top2 in Yeast
- 10:20, 8 August 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 in Yeast
- 22:54, 7 August 2017 (diff | hist) . . (+226) . . Macs2 (current)
- 14:40, 7 August 2017 (diff | hist) . . (+1,074) . . ChIP-Seq Top2 in Yeast
- 16:16, 4 August 2017 (diff | hist) . . (+385) . . Meryl (current)
- 16:07, 4 August 2017 (diff | hist) . . (+6,254) . . N Meryl (Created page with "= Introduction = This is a kmer coounting program, part of a larger suite of tools at kmer.sourceforge.net It's by Brian Walenz of Kanu (MinION genome assembly fame). = Hel...")
- 15:59, 4 August 2017 (diff | hist) . . (+13) . . Main Page
- 07:08, 4 August 2017 (diff | hist) . . (+34) . . JBrowse (current)
- 17:37, 30 July 2017 (diff | hist) . . (+462) . . ChIP-Seq Top2 in Yeast
- 17:35, 30 July 2017 (diff | hist) . . (+2) . . ChIP-Seq Top2 in Yeast
- 17:34, 30 July 2017 (diff | hist) . . (+134) . . ChIP-Seq Top2 in Yeast
- 17:23, 30 July 2017 (diff | hist) . . (+274) . . ChIP-Seq Top2 in Yeast
- 17:20, 30 July 2017 (diff | hist) . . (-40) . . Main Page
- 17:19, 30 July 2017 (diff | hist) . . (+425) . . N ChIP-Seq Top2 in Yeast (Created page with "= Introduction = This wiki page combines the two sequencing experiments of ChIP-Seq on yeast samples udring June / July 2017. * ChIP-Seq Top2 peak-calling * ChIP-Seq T...")
- 06:50, 21 July 2017 (diff | hist) . . (+466) . . ChIP-Seq Top2 peak-calling E2
- 20:27, 20 July 2017 (diff | hist) . . (-53) . . ChIP-Seq Top2 peak-calling E2
- 20:23, 20 July 2017 (diff | hist) . . (+1,245) . . ChIP-Seq Top2 peak-calling E2
- 12:35, 20 July 2017 (diff | hist) . . (+269) . . JBrowse
- 09:27, 20 July 2017 (diff | hist) . . (+1,318) . . SWATH-MS Data Analysis (current)
- 13:30, 18 July 2017 (diff | hist) . . (+127) . . FASTQC and MultiQC (current)
- 12:44, 18 July 2017 (diff | hist) . . (+365) . . FASTQC and MultiQC
- 16:37, 17 July 2017 (diff | hist) . . (+35) . . ChIP-Seq Top2 peak-calling E2
- 16:32, 17 July 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 peak-calling E2
- 16:29, 17 July 2017 (diff | hist) . . (+36) . . Main Page
- 16:26, 17 July 2017 (diff | hist) . . (-978) . . m ChIP-Seq Top2 peak-calling E2
- 16:08, 17 July 2017 (diff | hist) . . (+1,446) . . ChIP-Seq Top2 peak-calling E2
- 15:57, 17 July 2017 (diff | hist) . . (+4,892) . . N ChIP-Seq Top2 peak-calling E2 (Created page with "= Introduction = ChIP-Seq on Mutant vs. Wildtype, two states, 4 sets of pairs each, for a total of 16 pairs of paired-end datasets. The generic pipeline One of the authors...")
- 15:45, 17 July 2017 (diff | hist) . . (+13) . . ChIP-Seq Top2 peak-calling
- 13:58, 12 July 2017 (diff | hist) . . (+303) . . ChIP-Seq Top2 peak-calling
- 13:52, 12 July 2017 (diff | hist) . . (+289) . . ChIP-Seq Top2 peak-calling
- 13:46, 12 July 2017 (diff | hist) . . (0) . . N File:Uls1 teld0.png (current)
- 13:45, 12 July 2017 (diff | hist) . . (0) . . N File:Wt teld0.png (current)
- 09:55, 12 July 2017 (diff | hist) . . (0) . . Macs2
- 12:11, 7 July 2017 (diff | hist) . . (+2) . . CallSNPs.py
- 13:27, 6 July 2017 (diff | hist) . . (+414) . . JBrowse
- 12:50, 6 July 2017 (diff | hist) . . (+247) . . JBrowse
- 09:13, 6 July 2017 (diff | hist) . . (+42) . . N SWATH-MS Data Analysis (Created page with "= Introduction = = Links = * Pyprophet")
- 09:11, 6 July 2017 (diff | hist) . . (+47) . . Main Page
- 15:26, 4 July 2017 (diff | hist) . . (+13) . . RedHat
- 15:03, 4 July 2017 (diff | hist) . . (+287) . . RedHat
- 14:23, 4 July 2017 (diff | hist) . . (+581) . . SNP Analysis and phylogenetics (current)
- 13:47, 4 July 2017 (diff | hist) . . (+235) . . SNP Analysis and phylogenetics
- 13:35, 4 July 2017 (diff | hist) . . (+66) . . SNP Analysis and phylogenetics
- 13:19, 4 July 2017 (diff | hist) . . (+338) . . SNP Analysis and phylogenetics
- 13:10, 4 July 2017 (diff | hist) . . (+109) . . N SNP Analysis and phylogenetics (Created page with " = Links = == Andrew Rambaut = [https://groups.google.com/forum/#!topic/beast-users/V5vRghILMfw Says] that")
- 13:09, 4 July 2017 (diff | hist) . . (+37) . . Main Page
- 12:27, 29 June 2017 (diff | hist) . . (+253) . . Macs2
- 21:47, 28 June 2017 (diff | hist) . . (+1,904) . . Thor (current)
- 16:21, 21 June 2017 (diff | hist) . . (+1) . . Aspera (current)
- 16:21, 21 June 2017 (diff | hist) . . (+157) . . Aspera
- 16:13, 21 June 2017 (diff | hist) . . (+75) . . Aspera
- 14:13, 21 June 2017 (diff | hist) . . (+393) . . N Aspera (Created page with "= Introduction = It's probably the fastest way of downloading SRA files from the Short Read Archive. It's considerbaly faster than using ''''fastq-dump''' in its download mod...")
- 13:07, 21 June 2017 (diff | hist) . . (+14) . . Main Page
- 11:25, 21 June 2017 (diff | hist) . . (+92) . . JBrowse
- 16:48, 20 June 2017 (diff | hist) . . (+129) . . JBrowse
- 23:13, 18 June 2017 (diff | hist) . . (+1) . . Research Data Management (current)
- 22:05, 18 June 2017 (diff | hist) . . (+153) . . Research Data Management
- 14:36, 18 June 2017 (diff | hist) . . (+559) . . Research Data Management
- 14:08, 18 June 2017 (diff | hist) . . (+492) . . N Research Data Management (Created page with "= Introduction = The generation of genomic data has been expanding at ever-increasing rates whcih can result in a chaotic flood of datasets unless some discipline of Data Ama...")
- 14:04, 18 June 2017 (diff | hist) . . (+31) . . Main Page
- 15:14, 16 June 2017 (diff | hist) . . (+2,551) . . Thor
- 10:10, 16 June 2017 (diff | hist) . . (+67) . . JBrowse
- 09:53, 16 June 2017 (diff | hist) . . (+110) . . JBrowse
- 09:51, 16 June 2017 (diff | hist) . . (+187) . . JBrowse
- 09:26, 16 June 2017 (diff | hist) . . (+319) . . JBrowse
- 17:08, 15 June 2017 (diff | hist) . . (+534) . . N Bgenie (Created page with "= Introduction = bgen file processor from Jonathan Marchini = Usage = to load up the software: module load bgenie == typical use cases == (See the homepage n the Links...") (current)
- 16:51, 15 June 2017 (diff | hist) . . (+14) . . Main Page
- 14:06, 15 June 2017 (diff | hist) . . (+20) . . Main Page
- 14:05, 15 June 2017 (diff | hist) . . (+4,004) . . N KentUtils (Created page with "= Introduction = A myriad of bioinformatics tools from Jim Kent = The tools = addCols bedGraphToBigWig bigWigCorrelate chainStitchId faCmp...") (current)
- 13:45, 15 June 2017 (diff | hist) . . (0) . . Samtools (current)
- 13:45, 15 June 2017 (diff | hist) . . (+92) . . Samtools
- 12:22, 14 June 2017 (diff | hist) . . (+104) . . Deeptools (current)
- 12:20, 14 June 2017 (diff | hist) . . (+2,865) . . N Deeptools (Created page with "= Introduction = Deeptools is a python processing suite for bamfiles and renders them into genome browser track forms as such as bed and bigwig. It can be invoked in three w...")
- 12:12, 14 June 2017 (diff | hist) . . (+17) . . Main Page
- 15:32, 12 June 2017 (diff | hist) . . (+233) . . Bamtools (current)
- 13:27, 12 June 2017 (diff | hist) . . (-203) . . Bamtools
- 12:07, 12 June 2017 (diff | hist) . . (+8,922) . . N Bamtools (Created page with "= Introduction = The associated tool list is as follows: * convert * count * coverage * filter * header * index * merge * random * revert * sort * split * stats Introductio...")
- 11:59, 12 June 2017 (diff | hist) . . (+16) . . Main Page
- 10:01, 6 June 2017 (diff | hist) . . (+59) . . Thor
- 09:59, 6 June 2017 (diff | hist) . . (+1,660) . . Thor
- 09:21, 6 June 2017 (diff | hist) . . (+94) . . Thor
- 09:18, 6 June 2017 (diff | hist) . . (+2,081) . . Thor
- 16:15, 5 June 2017 (diff | hist) . . (-2,420) . . Macs2
- 16:12, 5 June 2017 (diff | hist) . . (+3,157) . . Macs2
- 16:05, 5 June 2017 (diff | hist) . . (+124) . . Macs2
- 15:54, 5 June 2017 (diff | hist) . . (0) . . Main Page
- 15:53, 5 June 2017 (diff | hist) . . (+43) . . Blat (current)
- 15:52, 5 June 2017 (diff | hist) . . (+768) . . N Blat (Created page with "= Introduction = BLAT is a tool from Jim Kent's stable at UCSD. In purpose it is very close to NCBI's BLAST, but it generally is easier in terms of switches and input options...")
- 15:42, 5 June 2017 (diff | hist) . . (+12) . . Main Page
- 15:23, 5 June 2017 (diff | hist) . . (+306) . . Thor
- 15:19, 5 June 2017 (diff | hist) . . (+462) . . Thor
- 13:33, 5 June 2017 (diff | hist) . . (+2,009) . . N Thor (Created page with "= Introduction = This is one of the newer Differential Peak callers from Costalab in Aachen. = Usage = == a first run == The first few runs are usually error-prone. Thor i...")
- 13:16, 5 June 2017 (diff | hist) . . (+12) . . Main Page
- 12:54, 5 June 2017 (diff | hist) . . (+50) . . m Macs2
- 10:53, 5 June 2017 (diff | hist) . . (+6,446) . . Macs2
- 08:49, 1 June 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 peak-calling
- 15:41, 31 May 2017 (diff | hist) . . (+429) . . ChIP-Seq Top2 peak-calling
- 15:12, 30 May 2017 (diff | hist) . . (+173) . . Bwa (current)
- 14:29, 30 May 2017 (diff | hist) . . (-5) . . ChIP-Seq Top2 peak-calling
- 14:14, 30 May 2017 (diff | hist) . . (+2,521) . . ChIP-Seq Top2 peak-calling
- 13:55, 30 May 2017 (diff | hist) . . (0) . . ChIP-Seq Top2 peak-calling
- 13:54, 30 May 2017 (diff | hist) . . (+1,148) . . ChIP-Seq Top2 peak-calling
- 13:50, 30 May 2017 (diff | hist) . . (+194) . . N ChIP-Seq Top2 peak-calling (Created page with "= Introduction = = Raw data description = = Raw dataset quality analysis = Using FASTQC and them MultiQC. Results linked [http:stab.st-andrews.ac.uk/stab/top2/fastqc.html...")
- 13:29, 30 May 2017 (diff | hist) . . (+33) . . Main Page (→Pipelines)
- 16:49, 22 May 2017 (diff | hist) . . (+3,216) . . N Macs2 (Created page with "= Introduction = One of the main programs used for peak-calling on ChIP-Seq alignments. = Usage = == Help file == Here is the programs help file obtained with the command...")
- 16:45, 22 May 2017 (diff | hist) . . (+13) . . Main Page
- 14:09, 14 May 2017 (diff | hist) . . (+13) . . Quality of Mapping Exercise (current)
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