File Changes for angie
switch to commits view, user indexv281_preview2 to v281_base (2013-03-19 to 2013-03-25) v281
- src/hg/lib/dbNsfpInterPro.as
- lines changed 8, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpLrt.as
- lines changed 21, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpMutationAssessor.as
- lines changed 18, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpMutationTaster.as
- lines changed 18, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpPolyPhen2.as
- lines changed 24, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpSeqChange.as
- lines changed 21, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpSift.as
- lines changed 15, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/lib/dbNsfpUniProt.as
- lines changed 9, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/makeDb/doc/hg19.txt
- lines changed 68, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- lines changed 2, context: html, text, full: html, text
Correcting the /hive path for dbNSFP2.0
- src/hg/utils/dbNsfpToBed.pl
- lines changed 379, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/utils/makefile
- lines changed 3, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
- src/hg/utils/mergeSortedBed3Plus.pl
- lines changed 64, context: html, text, full: html, text
Adding information from the Database of Non-Synonymous Functional Prediction(dbNSFP, https://sites.google.com/site/jpopgen/dbNSFP,
http://dbnsfp.houstonbioinformatics.org/dbNSFPzip/dbNSFP2.0.readme.txt).
dbNSFP2.0 contains precomputed predictions from a variety of tools of the
effects of all possible missense variants on protein-coding Gencode rel 9
(Ens 64) transcripts. For example, it contains scores and predictions
from SIFT, PolyPhen2 and similar tools (MutationTaster, MutationAssessor,
LRT), as well as GERP scores at CDS positions and associated domain
information from InterPro and IDs from UniProt. Each subset is
extracted into a bigBed or bigWig file so that users of the Variant
Annotation Integrator will be able to apply one or more of these
prediction methods to their variants.
refs #6152
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