Groups

OpenSequencing

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RV, Thomas Schwarzl3

7/26/16

DESeq2 normalized counts for HIerarchical clustering and PCA

Hi Tom, Thank you very much for validating and for the material. Best, Raghavee On Tuesday, 26 July

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DESeq2 normalized counts for HIerarchical clustering and PCA

Hi Tom, Thank you very much for validating and for the material. Best, Raghavee On Tuesday, 26 July

7/26/16

Kevin Rue-Albrecht2

3/2/15

OpenSequencing meeting - Monday 2nd March 14:00 - RNAseq & clustering

Dear all, Friendly reminder to all those interested in High-Throughput Sequencing that the OpenSeq

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OpenSequencing meeting - Monday 2nd March 14:00 - RNAseq & clustering

Dear all, Friendly reminder to all those interested in High-Throughput Sequencing that the OpenSeq

3/2/15

Kevin Rue, … Lisa Rogers6

4/28/14

Meeting Mo 28th April ?

Hi all, Quick reminder for the OpenSeq meeting today at 2pm in the Conway Interactive Hub. Best,

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Meeting Mo 28th April ?

Hi all, Quick reminder for the OpenSeq meeting today at 2pm in the Conway Interactive Hub. Best,

4/28/14

4/8/14

Fwd: A free informative directory for NGS and microarray data analysis

Hi all, Just a refresher about a website listing software for diifferent microarray and NGS

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Fwd: A free informative directory for NGS and microarray data analysis

Hi all, Just a refresher about a website listing software for diifferent microarray and NGS

4/8/14

3/19/14

Meeting 31/03 + quick demultiplexing question

Hi all, With Paddy's day, this week's a bit shorter. Plus some of us said they'll go to

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Meeting 31/03 + quick demultiplexing question

Hi all, With Paddy's day, this week's a bit shorter. Plus some of us said they'll go to

3/19/14

Adam Dinan, … Karsten Hokamp15

3/18/14

Looks good! I'm going as well. Registration deadline is today if anyone is interested... Karsten

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Looks good! I'm going as well. Registration deadline is today if anyone is interested... Karsten

3/18/14

Kevin Rue, Ricardo Segurado6

3/14/14

Expression profiles using ggplot + geom_smooth

I see. By the number of readings, I meant one reading at each time-point. ie some cells are drawn for

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Expression profiles using ggplot + geom_smooth

I see. By the number of readings, I meant one reading at each time-point. ie some cells are drawn for

3/14/14

adam....@ucdconnect.ie, … Markus Schroeder5

2/19/14

Meeting Monday 24th February

Thanks for sharing Markus, I have noticed that many papers, even in relatively high impact journals,

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Meeting Monday 24th February

Thanks for sharing Markus, I have noticed that many papers, even in relatively high impact journals,

2/19/14

Kevin Rue, Lisa Rogers3

12/9/13

Mixed cell-type samples deconvolution from expression data + tumor applications

Hi all, Sorry for the late notice, but let me confirm that today's meeting is cancelled. Now, I

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Mixed cell-type samples deconvolution from expression data + tumor applications

Hi all, Sorry for the late notice, but let me confirm that today's meeting is cancelled. Now, I

12/9/13

Lisa Rogers, Kevin Rue2

11/24/13

Possible Topics for Upcoming Meetings

HI all, Thank you Lisa for offering those topics. Remind me after December, 2nd, and we'll make

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Possible Topics for Upcoming Meetings

HI all, Thank you Lisa for offering those topics. Remind me after December, 2nd, and we'll make

11/24/13

Kevin Rue, … Yue Fan5

11/18/13

Meeting next Monday

Hi all, We are scheduled to have a meeting today at 2pm in the interactive hub, after the Monday PhD

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Meeting next Monday

Hi all, We are scheduled to have a meeting today at 2pm in the interactive hub, after the Monday PhD

11/18/13

Markus Schroeder

11/6/13

Systematic evaluation of spliced alignment programs for RNA-seq data

Systematic evaluation of spliced alignment programs for RNA-seq data www.nature.com/nmeth/journal/

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Systematic evaluation of spliced alignment programs for RNA-seq data

Systematic evaluation of spliced alignment programs for RNA-seq data www.nature.com/nmeth/journal/

11/6/13

11/4/13

Fwd: seminars today?

Hi all, As promised, here are the links to the three publications related to the "Regulatory

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Fwd: seminars today?

Hi all, As promised, here are the links to the three publications related to the "Regulatory

11/4/13

Kevin Rue, Karsten Hokamp2

11/4/13

Meeting Monday 4th November

Hi Kevin, Unfortunately, I won't be able to make it today. See you next time, Karsten On Thu, Oct

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Meeting Monday 4th November

Hi Kevin, Unfortunately, I won't be able to make it today. See you next time, Karsten On Thu, Oct

11/4/13

Kevin Rue, Karsten Hokamp2

10/25/13

Hi Kevin, Monday is pretty much the only days that works for me, so I would be in favour of moving it

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Hi Kevin, Monday is pretty much the only days that works for me, so I would be in favour of moving it

10/25/13

Kevin Rue, karen power4

10/11/13

Meeting agenda Monday 14th October

Great, Thanks Kevin. Karen On 11 October 2013 15:00, Kevin Rue <kevi...@ucdconnect.ie> wrote:

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Meeting agenda Monday 14th October

Great, Thanks Kevin. Karen On 11 October 2013 15:00, Kevin Rue <kevi...@ucdconnect.ie> wrote:

10/11/13

Markus Schroeder, Yue Fan3

10/7/13

GSNAP - another mapping tool

Hi, This is the cbio portal for easily accessing the TCGA datasets: http://www.cbioportal.org/public-

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GSNAP - another mapping tool

Hi, This is the cbio portal for easily accessing the TCGA datasets: http://www.cbioportal.org/public-

10/7/13

kevi...@ucdconnect.ie, Karsten Hokamp4

10/7/13

About resuming the OpenSequencing meetings...

Hi all, Even though there is no PhD Seminar today, I think we should maintain the OpenSequencing

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About resuming the OpenSequencing meetings...

Hi all, Even though there is no PhD Seminar today, I think we should maintain the OpenSequencing

10/7/13

9/24/13

Fwd: [bioinfo] Nouvel annuaire de logiciels pour l'analyse du séquençageà haut débit

Hi all, Someone in France developped a website to keep track of the available NGS tools, classified

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Fwd: [bioinfo] Nouvel annuaire de logiciels pour l'analyse du séquençageà haut débit

Hi all, Someone in France developped a website to keep track of the available NGS tools, classified

9/24/13

7/2/13

RNAseq Timeline

http://blog.sbgenomics.com/history-of-rna-seq/ RNA-Seq Interactive Literature Review Posted: Jun 25

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RNAseq Timeline

http://blog.sbgenomics.com/history-of-rna-seq/ RNA-Seq Interactive Literature Review Posted: Jun 25

7/2/13

adam....@ucdconnect.ie, … Kevin Rue8

6/20/13

Meeting Monday 24/06

Hi all, What's life without a Doodle, huh? ;) More seriously, a Doodle listing all Mondays until

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Meeting Monday 24/06

Hi all, What's life without a Doodle, huh? ;) More seriously, a Doodle listing all Mondays until

6/20/13

6/14/13

BGI seminar in UCD

Hi guys, The BGI seminar has been changed to seminar room 1 in Conway from 1-2pm today. Thanks.

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BGI seminar in UCD

Hi guys, The BGI seminar has been changed to seminar room 1 in Conway from 1-2pm today. Thanks.

6/14/13

Tom, … PubCrawler Administrator10

6/4/13

Hi all, thanks Karsten for the slides. Regarding the normalization issues, we did not discuss one

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Hi all, thanks Karsten for the slides. Regarding the normalization issues, we did not discuss one

6/4/13

5/13/13

Dear group, sequencing meeting is today from 2-3 pm, Seminar room 2. Thanks, Tom

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Dear group, sequencing meeting is today from 2-3 pm, Seminar room 2. Thanks, Tom

5/13/13

Markus Schroeder

5/7/13

CSHL - Tips for Preparing mRNA-Seq Libraries from Poly(A)+ mRNA

Tips for Preparing mRNA-Seq Libraries from Poly(A) + mRNA for Illumina Transcriptome High-Throughput

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CSHL - Tips for Preparing mRNA-Seq Libraries from Poly(A)+ mRNA

Tips for Preparing mRNA-Seq Libraries from Poly(A) + mRNA for Illumina Transcriptome High-Throughput

5/7/13

4/30/13

STAR presentation

Hi all, Just sharing the slides I showed you yesterday about STAR. Basically just excerpts from the

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STAR presentation

Hi all, Just sharing the slides I showed you yesterday about STAR. Basically just excerpts from the

4/30/13

Tom, … Nicolas Nalpas7

4/26/13

Great, Seminar Room 2 is booked. Have a great weekend! Tom On Friday, April 26, 2013 4:09:22 PM UTC+1

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Great, Seminar Room 2 is booked. Have a great weekend! Tom On Friday, April 26, 2013 4:09:22 PM UTC+1

4/26/13

Paul McGettigan

4/17/13

Another potential Miseq issue - with Nextera libraries

FYI Problem with read length longer than insert size generated by Nextera prep http://pathogenomics.

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Another potential Miseq issue - with Nextera libraries

FYI Problem with read length longer than insert size generated by Nextera prep http://pathogenomics.

4/17/13

Paul McGettigan, Adam Dinan2

4/17/13

Potential cross-contamination issues with MiSeq and fast HiSeq runs

Thanks for sharing Paul. We'll be using MiSeq and I wasn't aware of this. On 17 Apr 2013 08:

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Potential cross-contamination issues with MiSeq and fast HiSeq runs

Thanks for sharing Paul. We'll be using MiSeq and I wasn't aware of this. On 17 Apr 2013 08:

4/17/13

Paul McGettigan

4/15/13

TiTv ratio and RNA editing

Some links that are relevant to the discussion we had at the sequencing meeting: A discussion on

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TiTv ratio and RNA editing

Some links that are relevant to the discussion we had at the sequencing meeting: A discussion on

4/15/13

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