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Forum: Sample Prep / Library Generation 08-02-2014, 04:06 PM
Replies: 20
Views: 9,042
Posted By pmad
HI albireo, The package CexoR is also...

HI albireo,

The package CexoR is also available from Bioconductor for ChIP-exo peak calling (http://www.bioconductor.org/packages/devel/bioc/html/CexoR.html)

Pedro M
Forum: Literature Watch 04-02-2014, 09:23 AM
Replies: 0
Views: 2,248
Posted By pmad
PLoS Comput Biol: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Dat

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Bioinformatics 04-01-2014, 05:53 PM
Replies: 1
Views: 1,514
Posted By pmad
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li...

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Bioinformatics 04-01-2014, 05:49 PM
Replies: 1
Views: 1,426
Posted By pmad
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li...

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Bioinformatics 04-01-2014, 05:44 PM
Replies: 2
Views: 1,455
Posted By pmad
Arrow Want to learn how to analyze ChIP-seq data?

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Bioinformatics 04-01-2014, 05:25 PM
Replies: 3
Views: 3,491
Posted By pmad
we have recently published this guidelines: ...

we have recently published this guidelines:
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol...
Forum: Epigenetics 04-01-2014, 05:23 PM
Replies: 5
Views: 3,038
Posted By pmad
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li...

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Epigenetics 04-01-2014, 05:19 PM
Replies: 3
Views: 3,360
Posted By pmad
Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li...

Bailey T, Krajewski P, Ladunga I, Lefebvre C, Li Q, et al. (2013) Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data. PLoS Comput Biol 9(11): e1003326....
Forum: Epigenetics 10-21-2013, 04:12 PM
Replies: 0
Views: 1,358
Posted By pmad
DNaseR - DNase-seq digita genomic footprinting in R

Dear Bioinformatics community,

DNase-seq has been used to measure chromatin accessibility in a given
tissue or cell type on a genome-wide scale. In addition to DNaseI
hypersensitivite sites...
Forum: Epigenetics 10-21-2013, 04:04 PM
Replies: 0
Views: 1,979
Posted By pmad
CexoR: peak-pair calling in ChIP-exo data with replicates

Dear bioinformatics community,

If you are producing of analyzing ChIP-exo data (Rhee HS, Pugh BF, 2011, Cell 147:1408-19) with replicates, you might want to consider CexoR to uncover...
Forum: Sample Prep / Library Generation 10-21-2013, 03:56 PM
Replies: 2
Views: 3,816
Posted By pmad
Arrow Hi, If you are producing or analyzing ChIP-exo...

Hi,
If you are producing or analyzing ChIP-exo data (Rhee HS, Pugh BF, 2011, Cell 147:1408-19) with replicates, you might want to consider CexoR to uncover high-resolution protein-DNA interactions....
Forum: Bioinformatics 08-28-2013, 01:23 AM
Replies: 1
Views: 2,288
Posted By pmad
HI TFC, the Bioconductor package NarrowPeaks...

HI TFC,

the Bioconductor package NarrowPeaks

http://bioconductor.org/packages/release/bioc/html/NarrowPeaks.html

can handles comparison of bigWig files, but you will need to covert WIG to...
Forum: Bioinformatics 08-28-2013, 01:13 AM
Replies: 1
Views: 2,240
Posted By pmad
Narrow peaks in ChIP-seq WIG files

Hi John,

The Bioconductor package NarrowPeaks

http://bioconductor.org/packages/release/bioc/html/NarrowPeaks.html

is able to do what you mention. It takes a WIG files and analyzes the shape...
Forum: Bioinformatics 07-15-2010, 11:53 PM
Replies: 0
Views: 1,130
Posted By pmad
Question ChIPseq - Mathematical model for TF binding sites

Hello Seq community,

Does anyone have some source of information about modelling or identifying Transcription factor binding sites (enriched regions) apart from peaks criteria?


regards from...
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