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questions
0
votes
0
replies
169
views
Diffbind and DESeq2 comparison for differential sites
diffbind
deseq2
updated 5 weeks ago by
Ram
43k • written 6 weeks ago by
Ankit
▴ 500
0
votes
2
replies
257
views
Why counting by diffbind and featurecounts differ?
featurecounts
diffbind
7 weeks ago by
Ankit
▴ 500
0
votes
0
replies
263
views
Metagene / Average Profile Plots background correction required or not?
chip-seq
cutandrun
IgG
updated 5 months ago by
Ram
43k • written 5 months ago by
Ankit
▴ 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
732
views
Network analysis for two Factors
chip-seq
network-analysis
updated 8 months ago by
Ram
43k • written 15 months ago by
Ankit
▴ 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
colindaven
6.4k • written 2.6 years ago by
Ankit
▴ 500
6
votes
8
replies
1.4k
views
Make large matrix data interpretable. How?
R
matrix
updated 16 months ago by
Mensur Dlakic
★ 27k • written 16 months ago by
Ankit
▴ 500
1
vote
1
reply
574
views
How to determine methylation state of loci with C to T mutation?
Methylation
Mutation
DNA
updated 17 months ago by
Nana
▴ 30 • written 17 months ago by
Ankit
▴ 500
1
vote
2
replies
675
views
How to obtain GO:Slim terms for multiple GO:terms
GO
GOterms
GoSlim
20 months ago by
Ankit
▴ 500
5
votes
13
replies
2.4k
views
Tools to obtain sequence from bam file
sequencing
Bam
indels
updated 20 months ago by
cmdcolin
★ 3.8k • written 20 months ago by
Ankit
▴ 500
0
votes
2
replies
664
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
3.3k
views
7 follow
error while testing nextflow with --genome GRCh38
java
nextflow
updated 7 months ago by
Romina
• 0 • written 22 months ago by
Ankit
▴ 500
1
vote
5
replies
1.0k
views
Course/Book for biostatistics for researchers?
Biostatistics
updated 2.1 years ago by
GenoMax
142k • written 2.1 years ago by
Ankit
▴ 500
1
vote
6
replies
1.4k
views
Compare two scatter plots? Statistical test?
Scatter
Methylation
plot
2.2 years ago by
Ankit
▴ 500
1
vote
4
replies
1.0k
views
Software for multiple sequence alignment?
multiple
refrence
sequence
alignment
Fasta
2.4 years ago by
Ankit
▴ 500
0
votes
2
replies
940
views
How to get coordinate of genomic elements?
Repeats
Promoter
enhancer
CpG
2.3 years ago by
Ankit
▴ 500
0
votes
0
replies
448
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
GenoMax
142k • written 2.6 years ago by
Ankit
▴ 500
1
vote
4
replies
887
views
Extarct specific bases from BAM/SAM files
BAM
SAM
Bases
Extract
2.6 years ago by
Ankit
▴ 500
0
votes
0
replies
476
views
Low read coverage in Input: Peak calling/Filtering
reads
peaks
chip-seq
2.6 years ago by
Ankit
▴ 500
0
votes
5
replies
1.2k
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
832
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
836
views
Normalization of ChIP-Seq count matrix ??
count
normalise
chip-seq
updated 2.7 years ago by
ATpoint
82k • written 2.7 years ago by
Ankit
▴ 500
2
votes
7
replies
1.6k
views
Allele-Specific analysis for human WGBS data
allele
methylation
WGBS
allelespecific
dna
2.8 years ago by
Ankit
▴ 500
0
votes
1
reply
929
views
RnBeads Greedycut command ???
greedycut
rnbeads
array
methylation
updated 2.9 years ago by
almsu798
• 0 • written 3.6 years ago by
Ankit
▴ 500
4
votes
3
replies
5.7k
views
Appropriate Pipeline for Methylation EPIC array analysis?
epic
methylation arrays
updated 3.4 years ago by
BiostarGuardianAngel
▴ 20 • written 4.1 years ago by
Ankit
▴ 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 10 months ago by
Kermit
▴ 90 • written 3.5 years ago by
Ankit
▴ 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
d-cameron
★ 2.9k • written 3.5 years ago by
Ankit
▴ 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 3.9 years ago by
Sam
★ 4.7k • written 3.9 years ago by
Ankit
▴ 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
zx8754
11k • written 3.9 years ago by
Ankit
▴ 500
4
votes
10
replies
5.0k
views
Normalisation of RNAseq data and NOIseq
RNA-Seq
R
updated 4.0 years ago by
sokhnazainab
• 0 • written 6.0 years ago by
Ankit
▴ 500
4
votes
6
replies
2.2k
views
Deseq2 design matrix for multiple factors
RNA-Seq
deseq2
design matrix
updated 4.0 years ago by
ATpoint
82k • written 4.0 years ago by
Ankit
▴ 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 4 weeks ago by
Ram
43k • written 4.1 years ago by
Ankit
▴ 500
3
votes
16
replies
1.5k
views
How to bring all reads to the same length? Any tool?
Read-length
Bed
updated 11 months ago by
Ram
43k • written 4.3 years ago by
Ankit
▴ 500
1
vote
5
replies
986
views
RNASeq: Normalization of sample with allele specific duplication
RNA-Seq
normalisation
updated 3 months ago by
Ram
43k • written 4.6 years ago by
Ankit
▴ 500
13
votes
24
replies
3.5k
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
872
views
Detection of duplicated regions in RNA-seq data
RNA-Seq
duplication
updated 4.8 years ago by
Biostar
20 • written 4.8 years ago by
Ankit
▴ 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
jiaobingke
▴ 30 • written 5.5 years ago by
Ankit
▴ 500
0
votes
9
replies
1.3k
views
Barplot with base point as 0.5
barplot
updated 4.9 years ago by
H.Hasani
▴ 990 • written 4.9 years ago by
Ankit
▴ 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
Carambakaracho
★ 3.2k • written 4.9 years ago by
Ankit
▴ 500
2
votes
8
replies
4.5k
views
RNAseq: Fisher-exact test with Benjamini-Hochberg multiple-testing correction using R
RNA-Seq
Fisher exact test
Deseq2
updated 5.0 years ago by
GenoMax
142k • written 5.0 years ago by
Ankit
▴ 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
2.6k
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
gb
★ 2.2k • written 5.1 years ago by
Ankit
▴ 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 5.2 years ago by
Pierre Lindenbaum
161k • written 5.2 years ago by
Ankit
▴ 500
0
votes
3
replies
2.2k
views
Seqmonk: Bedgraph as input ? (EPIC methylation array data)
seqmonk
Bedgraph
methylation
probe design
updated 5.3 years ago by
Charles Warden
8.2k • written 5.4 years ago by
Ankit
▴ 500
5
votes
18
replies
5.9k
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
Eric Lim
★ 2.1k • written 5.9 years ago by
Ankit
▴ 500
52 results • Page
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