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0
votes
0
replies
158
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Diffbind and DESeq2 comparison for differential sites
diffbind deseq2
updated 4 weeks ago by 43k • written 5 weeks ago by ▴ 500
0
votes
2
replies
239
views
Why counting by diffbind and featurecounts differ?
featurecounts diffbind
6 weeks ago by Ankit ▴ 500
0
votes
0
replies
259
views
Metagene / Average Profile Plots background correction required or not?
chip-seq cutandrun IgG
updated 4 months ago by 43k • written 4 months ago by ▴ 500
6
votes
10
replies
1.2k
views
Making pairwise matrix using ChIP-Seq peak binding matrix in R
R matrix binding Chip-seq
8 months ago by Ankit ▴ 500
0
votes
2
replies
727
views
Network analysis for two Factors
chip-seq network-analysis
updated 8 months ago by 43k • written 15 months ago by ▴ 500
3
votes
6
replies
1.6k
views
Tools / Packages to assess allele specific methylation?
SNP Bismark allele-specific-methylation
updated 16 months ago by 6.4k • written 2.6 years ago by ▴ 500
6
votes
8
replies
1.4k
views
Make large matrix data interpretable. How?
R matrix
updated 16 months ago by ★ 27k • written 16 months ago by ▴ 500
1
vote
1
reply
570
views
How to determine methylation state of loci with C to T mutation?
Methylation Mutation DNA
updated 17 months ago by ▴ 30 • written 17 months ago by ▴ 500
1
vote
2
replies
670
views
How to obtain GO:Slim terms for multiple GO:terms
GO GOterms GoSlim
19 months ago by Ankit ▴ 500
5
votes
13
replies
2.3k
views
Tools to obtain sequence from bam file
sequencing Bam indels
updated 19 months ago by ★ 3.8k • written 20 months ago by ▴ 500
0
votes
2
replies
659
views
Genome-wide enrichment of histone marks and correlation with gene expression: Approach/Tools?
histone genomic rna-seq chip-seq chromhmm
21 months ago by Ankit ▴ 500
8
votes
13
replies
3.2k
views
7 follow
error while testing nextflow with --genome GRCh38
java nextflow
updated 6 months ago by • 0 • written 22 months ago by ▴ 500
1
vote
5
replies
990
views
Course/Book for biostatistics for researchers?
Biostatistics
updated 2.1 years ago by 142k • written 2.1 years ago by ▴ 500
1
vote
6
replies
1.4k
views
Compare two scatter plots? Statistical test?
Scatter Methylation plot
2.1 years ago by Ankit ▴ 500
1
vote
4
replies
998
views
Software for multiple sequence alignment?
multiple refrence sequence alignment Fasta
2.4 years ago by Ankit ▴ 500
0
votes
2
replies
934
views
How to get coordinate of genomic elements?
Repeats Promoter enhancer CpG
2.3 years ago by Ankit ▴ 500
0
votes
0
replies
445
views
How to obtain coordinates of genome-wide TADs (Topologically associating domains)?
Hi-C TAD genome
2.5 years ago by Ankit ▴ 500
2
votes
3
replies
1.1k
views
Extract specific reads from fastq or SRA
reads filter fastq sra
updated 2.5 years ago by 142k • written 2.5 years ago by ▴ 500
1
vote
4
replies
881
views
Extarct specific bases from BAM/SAM files
BAM SAM Bases Extract
2.5 years ago by Ankit ▴ 500
0
votes
0
replies
474
views
Low read coverage in Input: Peak calling/Filtering
reads peaks chip-seq
2.5 years ago by Ankit ▴ 500
0
votes
5
replies
1.1k
views
How to compare variability or calculate p-value in R within same group?
statistics test variability r
2.6 years ago by Ankit ▴ 500
0
votes
1
reply
827
views
txdb object for hg38 for CpG island, CpG shores, Shelves
annotations island CpG txdb CGI
2.6 years ago by Ankit ▴ 500
0
votes
1
reply
829
views
Normalization of ChIP-Seq count matrix ??
count normalise chip-seq
updated 2.6 years ago by 82k • written 2.6 years ago by ▴ 500
2
votes
7
replies
1.6k
views
Allele-Specific analysis for human WGBS data
allele methylation WGBS allelespecific dna
2.7 years ago by Ankit ▴ 500
0
votes
1
reply
922
views
RnBeads Greedycut command ???
greedycut rnbeads array methylation
updated 2.9 years ago by • 0 • written 3.6 years ago by ▴ 500
4
votes
3
replies
5.7k
views
Appropriate Pipeline for Methylation EPIC array analysis?
epic methylation arrays
updated 3.4 years ago by ▴ 20 • written 4.1 years ago by ▴ 500
0
votes
5
replies
1.5k
views
Prop.test for multiple rows/or full matrix and get p.values ?
prop.test statistics matrix
3.4 years ago by Ankit ▴ 500
9
votes
8
replies
1.8k
views
Quantify Isoforms in RNA-Seq data
RNA-Seq isoforms
updated 9 months ago by ▴ 90 • written 3.4 years ago by ▴ 500
4
votes
3
replies
1.1k
views
Tools to call Large indels/structural variations in whole genome BAM data of mouse strain?
indels structural variations whole genome mouse
updated 3.5 years ago by ★ 2.9k • written 3.5 years ago by ▴ 500
3
votes
3
replies
1.7k
views
Coordinates for genomic features?
gene utr promoter intron exon
3.7 years ago by Ankit ▴ 500
0
votes
2
replies
1.2k
views
Batch correction methylation array datasets. any packages?
methylation array batch
3.7 years ago by Ankit ▴ 500
2
votes
16
replies
6.7k
views
p value from multiple columns using R??
p.value statistical
updated 3.8 years ago by ★ 4.7k • written 3.8 years ago by ▴ 500
0
votes
5
replies
1.2k
views
How to get same reproducible value in R?
Champ Methylation arrays R Bioconductor
updated 3.9 years ago by 11k • written 3.9 years ago by ▴ 500
4
votes
10
replies
5.0k
views
Normalisation of RNAseq data and NOIseq
RNA-Seq R
updated 4.0 years ago by • 0 • written 6.0 years ago by ▴ 500
4
votes
6
replies
2.1k
views
Deseq2 design matrix for multiple factors
RNA-Seq deseq2 design matrix
updated 4.0 years ago by 82k • written 4.0 years ago by ▴ 500
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 21 days ago by 43k • written 4.0 years ago by ▴ 500
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length Bed
updated 10 months ago by 43k • written 4.3 years ago by ▴ 500
1
vote
5
replies
982
views
RNASeq: Normalization of sample with allele specific duplication
RNA-Seq normalisation
updated 3 months ago by 43k • written 4.6 years ago by ▴ 500
13
votes
24
replies
3.4k
views
Normalization of allele specific counts in RNA-seq
RNA-Seq allele-specific normalization SNP next-gen
4.7 years ago by Ankit ▴ 500
0
votes
2
replies
870
views
Detection of duplicated regions in RNA-seq data
RNA-Seq duplication
updated 4.7 years ago by 20 • written 4.8 years ago by ▴ 500
4
votes
4
replies
5.4k
views
How to extract uniquely mapped reads in Bowtie2
bowtie2 Bowtie2 alignment uniquely mapped reads
updated 4.9 years ago by ▴ 30 • written 5.5 years ago by ▴ 500
0
votes
9
replies
1.3k
views
Barplot with base point as 0.5
barplot
updated 4.9 years ago by ▴ 990 • written 4.9 years ago by ▴ 500
2
votes
13
replies
14k
views
Which statistical test to compare samples in Violin Plot?
violin plots statistics methylation
updated 4.9 years ago by ★ 3.2k • written 4.9 years ago by ▴ 500
2
votes
8
replies
4.4k
views
RNAseq: Fisher-exact test with Benjamini-Hochberg multiple-testing correction using R
RNA-Seq Fisher exact test Deseq2
updated 4.9 years ago by 142k • written 4.9 years ago by ▴ 500
0
votes
1
reply
1.7k
views
MACS2: Missing Peaks in Bed file but Present in Bedgraph/Bigwig?
macs2 ChIP-Seq bed bigwig allele-specific
5.0 years ago by Ankit ▴ 500
1
vote
2
replies
2.5k
views
Paired-end reads merge tool: Multiple @ lines in merged output of FLASH tool
flash paired-end read merge fastq
updated 5.1 years ago by ★ 2.2k • written 5.1 years ago by ▴ 500
6
votes
4
replies
2.4k
views
How to obtain SNP positions for specific mouse strain using VCF from Sanger Institute ftp server?
SNP VCF MOuse JF1 strain
updated 5.1 years ago by 161k • written 5.1 years ago by ▴ 500
0
votes
3
replies
2.2k
views
Seqmonk: Bedgraph as input ? (EPIC methylation array data)
seqmonk Bedgraph methylation probe design
updated 5.2 years ago by 8.2k • written 5.4 years ago by ▴ 500
5
votes
18
replies
5.8k
views
No mismatch allowed setting in Bowtie2 (-N 0 does not help)
Bowtie2 mismatch --score-min constant alignment
5.5 years ago by Ankit ▴ 500
2
votes
9
replies
1.9k
views
Effect of splice site mutations in mouse
RNA-Seq SNP splice sites
updated 5.9 years ago by ★ 2.1k • written 5.9 years ago by ▴ 500
52 results • Page 1 of 2
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