[Bioc-devel] New package for copy number detection from targeted sequencing using off-target reads

t.kuilman at nki.nl t.kuilman at nki.nl
Thu Apr 9 21:52:53 CEST 2015 

I am happy to announce that our CopywriteR tool is now available on the development branch of Bioconductor. CopywriteR extracts copy number information from targeted sequencing using off-target reads (for more information, see Kuilman et al, Genome Biology 16:49, 2015). This new method allows copy number detection in the absence of a reference, and circumvents some of the problems experienced when performing copy number analysis using on-target reads. CopywriteR can be applied to sequencing data from target enrichment on small gene panels, and to data obtained from various other techniques including chromatin immunoprecipitation. We believe that CopywriteR constitutes a widely applicable alternative to available tools.

We are looking forward to further improve the tool and would be happy to receive any feedback.

Best regards,

Thomas


--------------------------------------------------
Thomas Kuilman, PhD
Department of Molecular Oncology
Netherlands Cancer Institute
1066 CX Amsterdam
The Netherlands

Phone: +31-20-5121841

On 9 Apr 2015, at 21:05, <bioc-devel-request at r-project.org<mailto:bioc-devel-request at r-project.org>> <bioc-devel-request at r-project.org<mailto:bioc-devel-request at r-project.org>> wrote:

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Today's Topics:

  1. Announcing a new package: FlowRepositoryR (Josef Spidlen)
  2. Re: AnnotationHub: ExpressionSetResource Error in Docker
     devel_core (Vincent Carey)
  3. Re: AnnotationHub: ExpressionSetResource Error in Docker
     devel_core (Ludwig Geistlinger)
  4. Re: AnnotationHub: ExpressionSetResource Error in Docker
     devel_core (Martin Morgan)
  5. Fwd: Proposed biocViews for Hi-C assay (Nathaniel Hayden)
  6. Disabling commits to release today;       Update NEWS files,
     biocViews (Dan Tenenbaum)


----------------------------------------------------------------------

Message: 1
Date: Thu, 9 Apr 2015 05:19:00 -0700
From: Josef Spidlen <jspidlen at bccrc.ca<mailto:jspidlen at bccrc.ca>>
To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>
Subject: [Bioc-devel] Announcing a new package: FlowRepositoryR
Message-ID:
       <CAMeW6UjmAS4teXAOURTtMHnut977oCtWQ+KGnZXLAUkTDtPe+A at mail.gmail.com<mailto:CAMeW6UjmAS4teXAOURTtMHnut977oCtWQ+KGnZXLAUkTDtPe+A at mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"

Hello to those working with flow cytometry data,
we are excited to announce that our package, FlowRepositoryR, is now
available in BioConductor (devel). This package provides a light interface
to access FlowRepository (https://flowrepository.org/) data from within R.
FlowRepository is a public repository currently containing 456 flow
cytometry experiments (datasets). 218 of those are public at this point and
the numbers are growing as researchers keep submitting data as part of
their publications. FlowRepositoryR provides an easy access requiring very
little R experience. Basic operations, such as locating a dataset,
reviewing metadata and downloading files can be done in one or two lines of
code. I would argue that this can actually be easier, faster and more
reliable than having to open your web browser and start clicking around.
Access to both, public and private experiments is supported. All access is
read-only at this point, but we will look into adding write functionality
after the current BioConductor release.

Please let me know if you have any feedback, suggestions or feature
requests.

Cheers,
Josef

--
Josef Spidlen, Ph.D.
Staff Scientist, Terry Fox Laboratory, BC Cancer Agency
675 West 10th Avenue, Vancouver, BC, V5Z1L3, Canada
Tel. +1 604-675-8000, ex. 7755

       [[alternative HTML version deleted]]



------------------------------

Message: 2
Date: Thu, 9 Apr 2015 08:47:38 -0400
From: Vincent Carey <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>>
To: Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>>
Cc: "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error
       in      Docker devel_core
Message-ID:
       <CAANT7+XSLiFcNc_igq5yeeANZ7AwUrtKCtPEQb-r+2N4+XRzFA at mail.gmail.com<mailto:CAANT7+XSLiFcNc_igq5yeeANZ7AwUrtKCtPEQb-r+2N4+XRzFA at mail.gmail.com>>
Content-Type: text/plain; charset="UTF-8"

Please provide sessionInfo()

The class is defined in AnnotationHub in devel.  Perhaps it is not suitably
exported.

On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>> wrote:

Hi,

As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)

docker run -ti bioconductor/release_core R

and then executed

library(AnnotationHub)
hub <- AnnotationHub()

and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter, April 2015)

h <- hub[hub$rdataclass == "ExpressionSet"]
h
AnnotationHub with 1 record
# snapshotDate(): 2015-03-26
# names(): AH28855
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from The
C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
tum...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944 #
$sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["AH28855"]]'

and then tried to retrieve the record with either

h[["AH28855"]]

or

h[[1]]

I received the following error:

Error in value[[3L]](cond) :
 failed to create a 'AnnotationHubResource' instance for hub resource
   ?RNA-Sequencing and clinical data for 7706 tumor samples from The
   Cancer Genome Atlas? of class ExpressionSet; reason:
   ?ExpressionSetResource? is not a defined class


Did I do something wrong?
Thank you for your help,
Ludwig


--
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit f?r Bioinformatik
Institut f?r Informatik
Ludwig-Maximilians-Universit?t M?nchen
Amalienstrasse 17, 2. Stock, B?ro A201
80333 M?nchen

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel


       [[alternative HTML version deleted]]



------------------------------

Message: 3
Date: Thu, 9 Apr 2015 14:57:47 +0200
From: "Ludwig Geistlinger" <Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>>
To: "Vincent Carey" <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>>
Cc: "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error
       in Docker devel_core
Message-ID:
       <a54d06f2f2c62b0787353365b09e21b7.squirrel at imap.ifi.lmu.de<mailto:a54d06f2f2c62b0787353365b09e21b7.squirrel at imap.ifi.lmu.de>>
Content-Type: text/plain;charset=iso-8859-1

Here you go ...

sessionInfo()
R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
[1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8       LC_NAME=C
[9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AnnotationHub_1.99.72 BiocInstaller_1.17.5

loaded via a namespace (and not attached):
[1] Rcpp_0.11.5                  IRanges_2.1.43
[3] digest_0.6.8                 bitops_1.0-6
[5] mime_0.2                     GenomeInfoDb_1.3.13
[7] R6_2.0.1                     xtable_1.7-4
[9] DBI_0.3.1                    stats4_3.2.0
[11] RSQLite_1.0.0                httr_0.6.1
[13] S4Vectors_0.5.22             RJSONIO_1.3-0
[15] stringr_0.6.2                Biobase_2.27.2
[17] RCurl_1.95-4.5               shiny_0.11.1
[19] httpuv_1.3.2                 parallel_3.2.0
[21] BiocGenerics_0.13.6          AnnotationDbi_1.29.17
[23] htmltools_0.2.6              interactiveDisplayBase_1.5.1









Please provide sessionInfo()

The class is defined in AnnotationHub in devel.  Perhaps it is not
suitably
exported.

On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>> wrote:

Hi,

As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)

docker run -ti bioconductor/release_core R

and then executed

library(AnnotationHub)
hub <- AnnotationHub()

and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter, April 2015)

h <- hub[hub$rdataclass == "ExpressionSet"]
h
AnnotationHub with 1 record
# snapshotDate(): 2015-03-26
# names(): AH28855
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from
The
C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
tum...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944
#
$sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["AH28855"]]'

and then tried to retrieve the record with either

h[["AH28855"]]

or

h[[1]]

I received the following error:

Error in value[[3L]](cond) :
 failed to create a 'AnnotationHubResource' instance for hub resource
   ???RNA-Sequencing and clinical data for 7706 tumor samples from The
   Cancer Genome Atlas??? of class ExpressionSet; reason:
   ???ExpressionSetResource??? is not a defined class


Did I do something wrong?
Thank you for your help,
Ludwig


--
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit f??r Bioinformatik
Institut f??r Informatik
Ludwig-Maximilians-Universit??t M??nchen
Amalienstrasse 17, 2. Stock, B??ro A201
80333 M??nchen

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel





------------------------------

Message: 4
Date: Thu, 09 Apr 2015 08:47:14 -0700
From: Martin Morgan <mtmorgan at fredhutch.org<mailto:mtmorgan at fredhutch.org>>
To: Ludwig Geistlinger <Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>>,     Vincent
       Carey <stvjc at channing.harvard.edu<mailto:stvjc at channing.harvard.edu>>
Cc: "bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>" <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: Re: [Bioc-devel] AnnotationHub: ExpressionSetResource Error
       in Docker devel_core
Message-ID: <55269F02.4040207 at fredhutch.org<mailto:55269F02.4040207 at fredhutch.org>>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 04/09/2015 05:57 AM, Ludwig Geistlinger wrote:
Here you go ...

sessionInfo()
R Under development (unstable) (2015-03-09 r67969)
Platform: x86_64-unknown-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] AnnotationHub_1.99.72 BiocInstaller_1.17.5

Yes, this should be AnnotationHub 1.99.81. Should be installed with

  BiocInstaller::biocLite("AnnotationHub")

You can check that status of your Bioconductor installation with

  BiocInstaller::biocValid()


loaded via a namespace (and not attached):
 [1] Rcpp_0.11.5                  IRanges_2.1.43
 [3] digest_0.6.8                 bitops_1.0-6
 [5] mime_0.2                     GenomeInfoDb_1.3.13
 [7] R6_2.0.1                     xtable_1.7-4
 [9] DBI_0.3.1                    stats4_3.2.0
[11] RSQLite_1.0.0                httr_0.6.1
[13] S4Vectors_0.5.22             RJSONIO_1.3-0
[15] stringr_0.6.2                Biobase_2.27.2
[17] RCurl_1.95-4.5               shiny_0.11.1
[19] httpuv_1.3.2                 parallel_3.2.0
[21] BiocGenerics_0.13.6          AnnotationDbi_1.29.17
[23] htmltools_0.2.6              interactiveDisplayBase_1.5.1









Please provide sessionInfo()

The class is defined in AnnotationHub in devel.  Perhaps it is not
suitably
exported.

On Thu, Apr 9, 2015 at 5:33 AM, Ludwig Geistlinger <
Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>> wrote:

Hi,

As I pulled down the devel_core image (running boot2docker under OS X
Yosemite)

docker run -ti bioconductor/release_core R

and then executed

library(AnnotationHub)
hub <- AnnotationHub()

and selected the recently integrated GSE62944 TCGA dataset (announced in
the latest BioC newsletter, April 2015)

h <- hub[hub$rdataclass == "ExpressionSet"]
h
AnnotationHub with 1 record
# snapshotDate(): 2015-03-26
# names(): AH28855
# $dataprovider: GEO
# $species: Homo sapiens
# $rdataclass: ExpressionSet
# $title: RNA-Sequencing and clinical data for 7706 tumor samples from
The
C...
# $description: TCGA RNA-seq Rsubread-summarized raw count data for 7706
tum...
# $taxonomyid: 9606
# $genome: hg19
# $sourcetype: tar.gz
# $sourceurl: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944
#
$sourcelastmodifieddate: NA
# $sourcesize: NA
# $tags: TCGA, RNA-seq, Expression, Count
# retrieve record with 'object[["AH28855"]]'

and then tried to retrieve the record with either

h[["AH28855"]]

or

h[[1]]

I received the following error:

Error in value[[3L]](cond) :
  failed to create a 'AnnotationHubResource' instance for hub resource
    ???RNA-Sequencing and clinical data for 7706 tumor samples from The
    Cancer Genome Atlas??? of class ExpressionSet; reason:
    ???ExpressionSetResource??? is not a defined class


Did I do something wrong?
Thank you for your help,
Ludwig


--
Dipl.-Bioinf. Ludwig Geistlinger

Lehr- und Forschungseinheit f??r Bioinformatik
Institut f??r Informatik
Ludwig-Maximilians-Universit??t M??nchen
Amalienstrasse 17, 2. Stock, B??ro A201
80333 M??nchen

Tel.: 089-2180-4067
eMail: Ludwig.Geistlinger at bio.ifi.lmu.de<mailto:Ludwig.Geistlinger at bio.ifi.lmu.de>

_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



_______________________________________________
Bioc-devel at r-project.org<mailto:Bioc-devel at r-project.org> mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel



--
Computational Biology / Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N.
PO Box 19024 Seattle, WA 98109

Location: Arnold Building M1 B861
Phone: (206) 667-2793



------------------------------

Message: 5
Date: Thu, 09 Apr 2015 09:56:45 -0700
From: Nathaniel Hayden <nhayden at fredhutch.org<mailto:nhayden at fredhutch.org>>
To: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: [Bioc-devel] Fwd: Proposed biocViews for Hi-C assay
Message-ID: <5526AF4D.3040605 at fredhutch.org<mailto:5526AF4D.3040605 at fredhutch.org>>
Content-Type: text/plain; charset=utf-8; format=flowed

>From Aaron Lun.

On a related note, there's now a number of packages involved in
analyzing Hi-C data, e.g., GoTHiC, HiTC, GenomicInteractions and
diffHic. Would it be worth adding a BiocViews term for the Hi-C assay
(maybe under Technology -> Sequencing)?

Cheers,

Aaron

--
Aaron Lun
PhD student
Bioinformatics Division - Smyth Lab
Walter and Eliza Hall Institute of Medical Research



------------------------------

Message: 6
Date: Thu, 9 Apr 2015 12:05:28 -0700 (PDT)
From: Dan Tenenbaum <dtenenba at fredhutch.org<mailto:dtenenba at fredhutch.org>>
To: bioc-devel <bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>>
Subject: [Bioc-devel] Disabling commits to release today;       Update NEWS
       files, biocViews
Message-ID:
       <1142328456.1273934.1428606328397.JavaMail.root at fredhutch.org<mailto:1142328456.1273934.1428606328397.JavaMail.root at fredhutch.org>>
Content-Type: text/plain; charset=utf-8

Hi,

Just a reminder that according to the release schedule (http://bioconductor.org/developers/release-schedule/#april-9) we will be disabling commits to the current release (3.0) branch today at 4:20PM Seattle time and then running one last build for that branch.

Also, another reminder to please update your NEWS files if you want recent package NEWS to be included in our release announcement; this should be done by 5PM seattle time on Monday April 13th.

Also, please make sure your biocViews are up-to-date/valid/relevant. This is important
because this is one of the main ways people will find your package. Refer to:

http://bioconductor.org/developers/how-to/biocViews/

Thanks,
Dan



------------------------------

Subject: Digest Footer

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