TCGA DATA DOWNLOAD
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KanakaDurga Addepalli
May 9, 2012, 10:57:07 AM5/9/12
to cbiop...@googlegroups.com
Hi,
I am trying to download mutations for all cancer types, all genes.
I am not able to download without specifying the gene list.
Is there a way to download all mutations for all genes and all cancer types?
I also tried using R Package ‘cgdsr’, I need help in formulated the getProfileData command for all genes and all disease types.
Please help,
thanks,
Durga
Ethan Cerami
May 9, 2012, 12:13:20 PM5/9/12
to cbiop...@googlegroups.com, kadd...@masonlive.gmu.edu
Durga,
The portal is really oriented to downloading viewing "slices" of genomic data, for a specific set of genes.� Sounds like you want the complete download, which is available via the TCGA Data Portal:� https://tcga-data.nci.nih.gov/tcga/.� Have you tried that?
Ethan
The portal is really oriented to downloading viewing "slices" of genomic data, for a specific set of genes.� Sounds like you want the complete download, which is available via the TCGA Data Portal:� https://tcga-data.nci.nih.gov/tcga/.� Have you tried that?
Ethan
On 5/9/12 10:57 AM, KanakaDurga Addepalli wrote:
Hi,I am trying to download mutations for all cancer types, all genes.I am not able to download without specifying the gene list.Is there a way to download all mutations for all genes and all cancer types?
I also tried using R�Package �cgdsr�, I need help in formulated the�getProfileData command for all genes and all disease types.
Please help,thanks,Durga
Nikolaus Schultz
Jul 9, 2012, 9:51:06 AM7/9/12
to cbiop...@googlegroups.com, kadd...@masonlive.gmu.edu
Hi Durga,
The prostate data is here:
The sarcoma data is here:
Niki.
On Jul 8, 2012, at 11:00 PM, durga...@gmail.com wrote:
Thanks Ethan,
How about data other than from TCGA?
Can I get MSKCC data? like for example Prostrate cancer and sarcoma.
tx,
Durga
Nikolaus Schultz
Jan 4, 2013, 1:29:38 PM1/4/13
to KanakaDurga Addepalli, cbiop...@googlegroups.com
Hi Durga,
Below is the list of all genes with mutations.
CDH1
CTNNB1
EPHA1
EPHA5
EPHA7
ERBB4
FBXW7
IRS1
KIT
LTK
MOS
MST1R
NF1
NTRK1
PI4KA
PIK3CA
PTEN
PTK2B
RB1
SYK
TP53
Niki.
On Jan 4, 2013, at 1:13 PM, KanakaDurga Addepalli wrote:
> Hi Niki,
> A Happy new year to you first.
>
> This is a query I had sent back in July'2012.
>
> I have been working with the Prostate data and now need to download Sarcoma data.
> From you email below when I tried to download just the mutations from the portal, I am not able to.
> The reason is I do not have any specific list of genes.
>
> I am looking for the whole mutations set for sarcoma, so how do I download from the portal without giving any gene list?
> As for Prostate data, the first link you gave (email below) has a mutations link to download but not the sarcoma link/page.
>
> please help me get all the mutational data from the sarcoma data.
>
> thanks,
> Durga
>
Below is the list of all genes with mutations.
CDH1
CTNNB1
EPHA1
EPHA5
EPHA7
ERBB4
FBXW7
IRS1
KIT
LTK
MOS
MST1R
NF1
NTRK1
PI4KA
PIK3CA
PTEN
PTK2B
RB1
SYK
TP53
Niki.
On Jan 4, 2013, at 1:13 PM, KanakaDurga Addepalli wrote:
> Hi Niki,
> A Happy new year to you first.
>
> This is a query I had sent back in July'2012.
>
> I have been working with the Prostate data and now need to download Sarcoma data.
> From you email below when I tried to download just the mutations from the portal, I am not able to.
> The reason is I do not have any specific list of genes.
>
> I am looking for the whole mutations set for sarcoma, so how do I download from the portal without giving any gene list?
> As for Prostate data, the first link you gave (email below) has a mutations link to download but not the sarcoma link/page.
>
> please help me get all the mutational data from the sarcoma data.
>
> thanks,
> Durga
>
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