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530 results • Page
1 of 11
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0
votes
1
reply
38
views
Question about a public scRNA dataset(single end)?
publicdataset
scRNA
singlecell
updated 43 minutes ago by
ATpoint
60k • written 5 hours ago by
soda
• 0
0
votes
3
replies
99
views
Enrichment analysis and GSEA
GSEA
EnrichmentAnalysis
written 14 hours ago by
amrsalaheldin50
• 0
1
vote
1
reply
53
views
can i take promoter upstream 2kb from tss ?
upstream
promoter
2kb
tss
3 hours ago by
isha.lily20
▴ 10
0
votes
1
reply
86
views
InteractiveComplexHeatmap on DESeq2 object with more than 2 groups
DESeq2
InteractiveComplexHeatmap
heatmap
updated 4 hours ago by
jared.andrews07
★ 13k • written 12 hours ago by
miccoli.andrea89
• 0
0
votes
0
replies
46
views
Open issues in protein simulation in MC?
protein
protein-structure
protein-structure-prediction
10 hours ago by
user366312
▴ 10
0
votes
0
replies
80
views
Comparing expression of DEG gene in samples
DEG
limma
R
gene
13 hours ago by
Maryam
• 0
2
votes
4
replies
118
views
PCA to find clusters in gene expression data
expression
clustering
PCA
updated 13 hours ago by
ATpoint
60k • written 14 hours ago by
Hashirama
▴ 20
0
votes
1
reply
53
views
With the X.M.P of my memories activated the Biostar screen takes about 40 seconds to appear
Bios
XMP
RAM
Slowly
DDR4
offtopic
updated 51 minutes ago by
Jean-Karim Heriche
25k • written 15 hours ago by
sabrinalfmoura
• 0
0
votes
3
replies
95
views
Genes mutations in cancer
GSEA
cancer
analysis
enrichment
updated 14 hours ago by
Vincent Laufer
★ 1.8k • written 15 hours ago by
amrsalaheldin50
• 0
0
votes
3
replies
95
views
Extract bed file of uwanted chromosome names and positions from bam file
bedfile
samtools
bamfile
updated 13 hours ago by
Pierre Lindenbaum
144k • written 16 hours ago by
tien
• 0
0
votes
1
reply
83
views
CNV loss and high expression
Copy
expression
number
updated 13 hours ago by
iraun
★ 4.3k • written 15 hours ago by
Kasthuri
▴ 290
4
votes
1
reply
93
views
Is it okay to map reads from WES designed for GRCh37 to GRCh38?
exome
whole
sequencing
updated 17 hours ago by
Pierre Lindenbaum
144k • written 17 hours ago by
samuelandjw
▴ 210
0
votes
0
replies
55
views
choose databbases in variant annotation
annotate
Annovar
18 hours ago by
arwa.ahmad95
• 0
0
votes
1
reply
166
views
Which pipeline to choose for RNA velocity
Seurat
genomics
seq
velocity
RNA
10x
scRNA
updated 18 hours ago by
rpolicastro
8.1k • written 1 day ago by
Meghamsh
• 0
2
votes
5
replies
115
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
19 hours ago by
soheil
• 0
4
votes
6
replies
195
views
Difference between commands [bowtie2, samtools]
bowtie2
samtools
updated 13 hours ago by
iraun
★ 4.3k • written 23 hours ago by
Jimpix
• 0
0
votes
2
replies
93
views
Mirdeep not giving results.
novel
Mirdeep
miRNA
sequence
RNA
20 hours ago by
A. Blue
• 0
0
votes
1
reply
101
views
mkdir: cannot create directory ‘/home/neel@m95/Desktop/AMR/cgview_comparison_tool/cog_db’: Permission denied
CGView
CCT
updated 1 day ago by
cpad0112
20k • written 1 day ago by
Neel
• 0
0
votes
2
replies
240
views
Is it correct to use Tophat2 directly followed by Cuffquant to only align to the reference transcriptomes without wishing to assemble new transcripts?
Tophat2
Cuffquant
Cufflinks
1 day ago by
zoukai3412085
• 0
0
votes
2
replies
111
views
minimum number of protein sequences for a sequence logo
logo
1 day ago by
Stefano
• 0
2
votes
1
reply
1.0k
views
How to choose threshold for filtering low counts before Voom transformation?
RNA-Seq
R
limma
voom
updated 1 day ago by
Gordon Smyth
★ 4.4k • written 21 months ago by
ihc.europa
▴ 20
0
votes
1
reply
90
views
browser to visualize single cell data
scATAC-seq
updated 1 day ago by
cpad0112
20k • written 1 day ago by
Bogdan
★ 1.2k
0
votes
0
replies
71
views
NCBI tblastx remote
NCBI
remote
tblastx
1 day ago by
ailton
• 0
1
vote
1
reply
125
views
Handling NA values in limma's voom design matrix
rna-seq
voom
design.matrix
limma
NA
updated 20 hours ago by
ATpoint
60k • written 1 day ago by
rubic
▴ 240
3
votes
5
replies
280
views
Issue with trend line and confidence interval
geom_smooth
ggplot
updated 10 hours ago by
Jeremy
▴ 110 • written 2 days ago by
pdhrati02
▴ 30
0
votes
1
reply
141
views
WGCNA functions not found
wgcna
updated 1 day ago by
Shred
▴ 620 • written 1 day ago by
jabbari.parnian
▴ 20
2
votes
2
replies
237
views
Determine sex/ gender of a mouse cell line via sequencing data
sequencing
line
cell
1 day ago by
cwwong13
▴ 10
0
votes
4
replies
207
views
ORFfinder length filter
Filter
ORFfinder
updated 1 day ago by
Pierre Lindenbaum
144k • written 1 day ago by
Princy
▴ 40
1
vote
1
reply
143
views
Tool:
Roakvar: do genomic variant analyses with R
oakvar
genomics
roakvar
variant
analysis
updated 1 day ago by
cpad0112
20k • written 1 day ago by
Ryangguk Kim
▴ 60
2
votes
5
replies
239
views
How to convert fastq to BAM
fastq
bam
updated 1 day ago by
cmdcolin
★ 2.1k • written 1 day ago by
ja4123
• 0
0
votes
0
replies
87
views
how to create "sample file" for the qAlign() function after trimming the reads in R
alignment
ChIP-Seq
R
RNA-Seq
1 day ago by
layan.essam
• 0
0
votes
1
reply
150
views
RNAseq on dataset containing RPKM
expression
differential
updated 1 day ago by
ATpoint
60k • written 1 day ago by
iibrams07
▴ 10
0
votes
0
replies
89
views
How to get list of blood-expressed Fantom 5 enhancers?
bioinformatics
2 days ago by
samuelandjw
▴ 210
2
votes
4
replies
260
views
VCF Statistics
VCF
satistics
variants
stats
updated 1 day ago by
Pierre Lindenbaum
144k • written 4 days ago by
vlip
• 0
0
votes
3
replies
224
views
plink bim file stops at chrM
plink
chr
bim
updated 13 hours ago by
chrchang523
9.2k • written 2 days ago by
rturba
▴ 10
2
votes
1
reply
253
views
How to run ROSE by a wet-lab research
ROSE
updated 2 days ago by
rpolicastro
8.1k • written 8 weeks ago by
b8921019
• 0
0
votes
3
replies
222
views
Connection refused FTPI NCBI NR DATABASE
NCBI
refused
Connection
FTPI
updated 1 day ago by
GenoMax
115k • written 2 days ago by
LEIDY PAOLA
• 0
0
votes
5
replies
305
views
different number of samples from each individual
statistics
updated 2 days ago by
Kevin Blighe
81k • written 2 days ago by
leranwangcs
▴ 60
6
votes
6
replies
308
views
For loop in R
Kegg
clusterprofiler
R
updated 1 day ago by
cpad0112
20k • written 2 days ago by
AP
▴ 70
1
vote
2
replies
175
views
SnpEff filter PASS - what are the QC filters?
SnpEff
2 days ago by
Jennifer
• 0
0
votes
0
replies
118
views
error in getting mutation data
TCGA
BRCA
Mutation
updated 2 days ago by
Ram
36k • written 2 days ago by
StartR
▴ 20
0
votes
1
reply
577
views
Transdecoder output for differential expression analyses: header problem
RNA-Seq
Assembly
software error
genome
alignment
updated 2 days ago by
sofia
• 0 • written 17 months ago by
1215045934
▴ 40
1
vote
1
reply
130
views
How to drop specific sites from VCFs?
vcf
updated 2 days ago by
GenoMax
115k • written 2 days ago by
kynnjo
▴ 50
0
votes
4
replies
370
views
function GDCquery_Maf error
GDCquery_Maf
R
maftools
updated 2 days ago by
StartR
▴ 20 • written 4 weeks ago by
Negatyvna
• 0
6
votes
4
replies
241
views
Trimming RNAseq data for transcriptome assembly
Rna
seq
updated 1 day ago by
lieven.sterck
13k • written 2 days ago by
al_capone13
• 0
3
votes
3
replies
215
views
STAR align quantMode
gene
genecounts
counts
quantmode
star
updated 2 days ago by
binodregmi30
▴ 10 • written 2 days ago by
a_bis
▴ 20
0
votes
3
replies
174
views
Statistical methods to determine descrimimant variables between two groups
multivariate
R
statistics
Univariate
updated 2 days ago by
Jean-Karim Heriche
25k • written 2 days ago by
Bioinfo
▴ 20
1
vote
1
reply
129
views
Plink v1.9: Order of SNPs when extracting from file
plink
updated 2 days ago by
chrchang523
9.2k • written 2 days ago by
docj
• 0
2
votes
5
replies
262
views
What does the sixth column of the unstranded bed file show +-?
bam
unstranded
RNA-seq
bedtools
star
2 days ago by
5Tony
• 0
0
votes
2
replies
161
views
Marking Duplicate reads in deep sequencing data
WES
MarkDuplicates
duplicates
sequencing
BAM
1 day ago by
Tom
• 0
530 results • Page
1 of 11
Recent Votes
C: Demultiplexing reads with index present in the labels
A: How to "discover" read structure and barcodes given Illumina sequencing run dire
how to combine RNA seq data from 4 lanes
Convert read counts to RPKM or TPM values: Numbers don't look right?
Answer: can i take promoter upstream 2kb from tss ?
Answer: PCA to find clusters in gene expression data
Comment: Is it okay to map reads from WES designed for GRCh37 to GRCh38?
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Teacher
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ATpoint
60k
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to
Juke34
★ 6.9k
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to
igor
12k
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to
gtasource
▴ 60
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Pierre Lindenbaum
144k
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wiscoyogi
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Kasthuri
▴ 290
Recent Replies
Answer: Question about a public scRNA dataset(single end)?
by
ATpoint
60k
Seems indeed that R1 is missing, making the data basically useless. I would contact the authors.
Comment: With the X.M.P of my memories activated the Biostar screen takes about 40 second
by
Jean-Karim Heriche
25k
This post does not fit the theme of this forum.
Answer: Enrichment analysis and GSEA
by
jared.andrews07
★ 13k
GSEA stands for gene set enrichment analysis. It's not clear what you mean by "enrichment analysis" here. Regardless, GSEA at minimum needs…
Answer: can i take promoter upstream 2kb from tss ?
by
jared.andrews07
★ 13k
Yes, that is a fairly common cutoff for defining a promoter region.
Answer: InteractiveComplexHeatmap on DESeq2 object with more than 2 groups
by
jared.andrews07
★ 13k
The comparison shown is just for whatever comes out of `results(dds)`. It's not going to combine different comparisons for you, but it will…
Comment: how can I save the distance matrix in csv file?
by
KHiLLCHiNG
• 0
Thank you, Joe! I really missedthe `.matrix` attribute. And you reminded me of it and I transfered the matrix into a dataframe and then wr…
Comment: Issue with trend line and confidence interval
by
Jeremy
▴ 110
Try setting the method to generalized additive model (GAM). gam = ggplot(df, aes(x = Time2, y = Abundance, group = Group, color = Grou…
Comment: How to make a read count matrix from multiple bed files generated by ROSE
by
ksong
▴ 20
Hello my friend, I know this post is old. However I plan to do the exactly the same thing recently: generating normalized count matrix usin…
Comment: plink bim file stops at chrM
by
chrchang523
9.2k
Please post or send me a VCF file that illustrates what you're talking about, along with the plink .log file.
Comment: PCA to find clusters in gene expression data
by
ATpoint
60k
I guess you want sifferential genes? Check tools wuch as limma-voom.
Comment: Incomplete TE identification by repeatmasker
by
samuel.a.odonnell
▴ 330
So all the repeats identified by RepeatModeler are labelled "unknown"? Otherwise the fasta header for each sequence would have an indicatio…
Comment: CNV loss and high expression
by
iraun
★ 4.3k
I guess you have normalized the expression values between those samples in order to make the comparison?
Comment: Difference between commands [bowtie2, samtools]
by
iraun
★ 4.3k
Hi! No problem. I have never used -u myself. [Here][1] you can read the manual of samtools, which says the same as what @GenoMax has pointe…
Comment: Extract bed file of uwanted chromosome names and positions from bam file
by
Pierre Lindenbaum
144k
find the fasta reference file, index it with `samtools faidx /path/to/ref.fasta`
Comment: PCA to find clusters in gene expression data
by
4galaxy77
★ 1.6k
This is a case where you don’t need a statistical test to find out whether the clusters are distinct.
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