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Showing top results for tag: Methylation • reset
0
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0
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55
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Problem with minfi package
minfi methylation analysis package DNA
updated 3 days ago by 107k • written 3 days ago by • 0
0
votes
0
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41
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Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark
methylation
7 days ago by pixie@bioinfo ★ 1.4k
4
votes
4
replies
267
views
Good or bad idea to annotate with newer genome build?
array methylation beadchip build annotation
17 days ago by Pratik Mehta ▴ 580
1
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6
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387
views
Methylkit (differential methylation analysis) error in data frame
methylation differential analysis R methylkit
18 days ago by harshraje19 ▴ 40
0
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0
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118
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IPD values from ipdsummary, methylation analysis using PacBio
methylation DNAsequencing IPD m4C m6A
24 days ago by Buffo ★ 1.9k
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0
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91
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Using MethylKit with gemBS output files
WGBS DMR Methylation
25 days ago by N • 0
0
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0
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79
views
Error in methyl kit (differential methylation analysis) in R
epeigenetics methylation differential analysis R methylkit DNA
26 days ago by harshraje19 ▴ 40
3
votes
4
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1.9k
views
Reading methylation without IDAT files downloaded from GEO
Methylation Gene expression omnibus GEO minfi
updated 27 days ago by ▴ 10 • written 3.0 years ago by ▴ 270
1
vote
2
replies
209
views
methylation beta distribution (minfi generated)
array methylation
8 days ago by anikb ▴ 40
0
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0
replies
97
views
DNA methylation EPIC array and ChromHMM
chromHMM methylation binary R regions DNA
4 weeks ago by macsuejacques • 0
5
votes
3
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451
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Is removing strand information when obtaining intergenic regions from GRanges necessary?
GenomicRanges methylation strand intergenic genic
updated 4 weeks ago by 6.9k • written 5 weeks ago by ▴ 580
6
votes
4
replies
543
views
Why do I get a big log fold change but small mean change in b value when plotting differential methylation?
differential volcano methylation
updated 6 weeks ago by ★ 3.4k • written 6 weeks ago by • 0
2
votes
7
replies
458
views
Allele-Specific analysis for human WGBS data
allele methylation WGBS allelespecific dna
6 weeks ago by Ankit ▴ 280
2
votes
3
replies
272
views
How to plot/combine biological replicates on a genomic features plot for methylated array?
array methylation beadchip plot features genomic
updated 8 weeks ago by ★ 1.3k • written 8 weeks ago by ▴ 580
3
votes
2
replies
288
views
What cut-offs to use for Genomic Features Pie Chart for Methylation Array Data?
beadchip array methylation
8 weeks ago by Pratik Mehta ▴ 580
0
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0
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98
views
Comparative methylation between two isogenic strains of E coli
nanopolish isogenic methylation
9 weeks ago by lkthomp06 • 0
0
votes
2
replies
237
views
What are the conventions/how to tell what a GSM has had done to it?
GSE GSM methylation minfi GEOquery
updated 9 weeks ago by • 0 • written 3 months ago by • 0
3
votes
4
replies
327
views
how to detect non CpG methylation probes ?
DNAmethylation methylation infinium450k microarray minfi R
11 weeks ago by takoyaki ▴ 90
0
votes
1
reply
371
views
RnBeads Greedycut command ???
greedycut rnbeads array methylation
updated 12 weeks ago by • 0 • written 12 months ago by ▴ 280
0
votes
0
replies
111
views
Read trimming in BS-Seq
Methylation BS-Seq Bismark WGBS
3 months ago by Arindam Ghosh ▴ 380
3
votes
7
replies
884
views
7 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation Experience Illumina Mouse
updated 5 days ago by • 0 • written 4 months ago by ▴ 20
2
votes
1
reply
156
views
Package/script for random DNA generation with a pattern!
DNA regex methylation
updated 3 months ago by ★ 1.5k • written 3 months ago by ★ 1.6k
0
votes
0
replies
127
views
Bismark Report Merging
wbgs methylation bismark
3 months ago by maxrhighsmith • 0
22
votes
1
reply
4.1k
views
Tutorial: Methylation Analysis Tutorial in R_part1
Tutorial cancer methylation R
updated 4 months ago by ▴ 30 • written 11 months ago by ★ 1.7k
0
votes
0
replies
130
views
Extracting Promoter Sequence from reverse Strand using NCBI Entrez and Eukaryotic Promoter Database?
Database design Promoter strand gene sequence Eukarytoic methylation Primer reverse
4 months ago by Lys • 0
1
vote
4
replies
796
views
How to calculate differential methylation from nanopore reads?
sequencing methylation
4 months ago by O.rka ▴ 380
0
votes
0
replies
142
views
News: Comprehensive benchmarking of software for mapping whole genome bisulfite data
Methylation NGS Epigenetics Bisulfite
4 months ago by David Langenberger 9.6k
0
votes
0
replies
115
views
How to analyze MBD-Seq data?
CpG methyl islands MBD-Seq methylation
4 months ago by dagsbio ▴ 20
1
vote
1
reply
183
views
How to overcome issue linked to loading big R object
R methylation bioconductor minfi
4 months ago by Fede_Santos95 ▴ 10
0
votes
2
replies
239
views
Gene ontology analysis
enrichment methylation gene_identifier
3 months ago by Kajol • 0
0
votes
0
replies
158
views
correlation of WGBS dataset and RNAseq dataset
transcription methylation
5 months ago by frylhc • 0
0
votes
0
replies
182
views
UK Biobank methylation data
DNA biobank methylation
5 months ago by Ivan • 0
0
votes
0
replies
135
views
Probabilistic modeling of CpG ß-values
statistics epigenetics methylation
updated 3 months ago by 34k • written 5 months ago by ▴ 70
1
vote
0
replies
232
views
Methylation frequency + and - strand
methylation Bismark
5 months ago by Palgrave ▴ 30
0
votes
5
replies
717
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Limma experiment design and making contrasts
limma methylation 450k
5 months ago by kra277 • 0
0
votes
0
replies
202
views
Copy number Variation frequency plot
CNV EPIC 450k methylation
5 months ago by user911111111 • 0
0
votes
0
replies
160
views
How to calculate power to detect mQTLs?
Illumina power mqtl methylation
5 months ago by anamaria ▴ 160
0
votes
0
replies
220
views
Job: Postdoc openings @ NYC: Epigenetics / Long Reads / Microbiome
sequencing RNAseq microbiome methylation
5 months ago by fanggang ▴ 100
1
vote
0
replies
208
views
Bedmethyl
methylation bedmethyl
6 months ago by alorsonmethyle ▴ 40
0
votes
0
replies
187
views
How can I download Methylation data for MethylMix package. (unusual error popped)
R software error MethylMix Methylation
6 months ago by shlokanegi.phe18 • 0
14
votes
2
replies
1.3k
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
6 months ago by Hamid Ghaedi ★ 1.7k
0
votes
0
replies
290
views
Job: Postdoctoral Research Fellow position in Molecular Biology
RNA nanopore sequencing biology methylation Job
6 months ago by adnan.niazi • 0
0
votes
2
replies
215
views
Violation of Independence test for differential methylation (DM)
methylation differential methylation
6 months ago by CY ▴ 610
0
votes
0
replies
278
views
TCGA methylation data analysis. beta values to differentially regulated CpGs
methylation beta values DMP
7 months ago by english.server ▴ 250
1
vote
5
replies
614
views
RnBeads error running rnb.run.dj()
rnbeads methylation bioinformatics ngs help
updated 7 months ago by ▴ 30 • written 7 months ago by ▴ 60
0
votes
0
replies
445
views
Surrogate variable, celltype composition correction and overfitting in DNA methylation data
array sva limma methylation
8 months ago by Papyrus ★ 1.3k
0
votes
0
replies
435
views
News: DNA Methylation Data Analysis Workshop (April 12-15, 2021 in Berlin)
Epgenetics Bisulfite Methylation News
8 months ago by David Langenberger 9.6k
0
votes
0
replies
400
views
Is there any method to compare t-SNE plot drawn by same samples and different standard?
EPIC t-sne Methylation array Methylation
8 months ago by kwanghoon ▴ 20
0
votes
3
replies
270
views
DNA Methylation file read
R methylation
updated 8 months ago by 5.9k • written 8 months ago by • 0
0
votes
1
reply
337
views
Genomic position to genomic feature
genome DMR Methylation
8 months ago by irfanwustl ▴ 20
50 results • Page 1 of 1
Recent Votes
Comment: Weird error from BWA and BOWTIE2
C: Sequence Length Distribution From A Fastq File
Answer: How can I extract upstream regions in fasta for all blastx hits locally performe
C: What Are The Most Common Stupid Mistakes In Bioinformatics?
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE
A: Automatic Outlier Detection for RNA-seq data
A: ATAC-seq sample normalization (quantil normalization)
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Recent Replies
Comment: Importing multiple datasets into one folder by Mensur Dlakic ★ 13k
Are you interested in moving all `.fastq` files from various folders into one? Because that can be done with a single command, but not sure…
Comment: Beginner problem: install python3.7.12 but py_available() still return FALSE by Ram 34k
Please do not delete the post after it has received feedback.
Comment: How can I know the BLAST percentage from kraken2 files ? by h.mon 33k
You can't. In no moment whatsoever Kraken2 performs an alignment. Morever, BLAST is BLAST, Kraken2 is Kraken2, they are not related and p…
Comment: Importing multiple datasets into one folder by GenoMax 107k
Galaxy specific questions are best asked on their dedicated support forum: https://help.galaxyproject.org/
Comment: circulating toumor DNA by GenoMax 107k
Since all cells shed [** free DNA**][1] that circulates (`cfDNA`) (including tumor cells) I don't know if there needs to be a separate data…
Comment: Automatic Outlier Detection for RNA-seq data by Kevin Blighe 77k
There is actually, well, a sort of citation off the top of my head. Please see the PLINK documentation (section '*Outlier detection diagnos…
Answer: Batch effects by swbarnes2 11k
It's always safest to get raw data and normalize it yourself. If one dataset is control, and the other is not, there is no magic way to …
Comment: GREP from multiFasta file and keep headers by Pierre Lindenbaum 138k
your command line with `grep` **implies** that each record in your fasta file takes only two line (?). One line for the header, and one lin…
Answer: In what way should cellranger count be performed , when there are multiple runs by swbarnes2 11k
If you did **one** library prep and ran that one library prep multiple times, it is probably easiest to combine the fastqs (make sure to gi…
Comment: Splice aware vs splice unaware aligners? by swbarnes2 11k
I think for time's sake a not-splice aware aligner isn't going to search horribly far away for the other half of a read, while a splice-awa…
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
Anyway, thanks your reply!
Comment: Automatic Outlier Detection for RNA-seq data by simplitia ▴ 60
@kevin thank is a great answer. We are having the same issue with outliers. With the 2nd part using > 3 SD; do you have a reference for …
Comment: How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to by Papyrus ★ 1.3k
Take a look at the [DiffBind][1] R package (which internally uses `DESeq2`, or `edgeR`), the tutorial [vignette][2] is quite extensive. …
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by Sashu • 0
I forget to tell that I have followed the error message but this problem still existed...
Comment: Beginner problem: installed python3.7.12 but py_available() return FALSE by jared.andrews07 ★ 11k
Follow the error message. Allow reticulate to handle the python environment itself.
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