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896 results • Page
1 of 18
Sort: replies
Rank
Views
Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
20 days ago by
Kevin Blighe
88k
10
votes
36
replies
5.9k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA
batch-effect
DESeq2
R
updated 28 days ago by
Ram
43k • written 5.7 years ago by
Kristin Muench
▴ 620
29
votes
28
replies
34k
views
11 follow
Split Fastq Files Into Chunks Of 1M Reads
split
fastq
updated 13 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 27 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
38
votes
24
replies
2.2k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 15 days ago by
i.sudbery
19k • written 18 days ago by
noodle
▴ 580
23
votes
23
replies
9.9k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq
removeBatchEffect
batch-effect
edger
updated 28 days ago by
Ram
43k • written 5.4 years ago by
iraia.munoa
▴ 130
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
4 days ago by
vytarasov
▴ 180
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva
combat
batch-effect
updated 28 days ago by
Ram
43k • written 6.8 years ago by
lessismore
★ 1.3k
22
votes
18
replies
6.2k
views
about batch correction in scRNA-seq
scRNA
scRNA-seq
batch-effect
updated 27 days ago by
Ram
43k • written 4.6 years ago by
Bogdan
★ 1.4k
6
votes
17
replies
6.6k
views
Can you add a label key to heatscatter plot in R?
heatscatter
visualization
R
updated 28 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
8
votes
16
replies
1.2k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 19 days ago by
bk11
★ 2.4k • written 9 weeks ago by
Sofia
• 0
34
votes
16
replies
21k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 26 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
7
votes
16
replies
918
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
16 days ago by
Ruqaiya
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 8 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
4
votes
15
replies
1.7k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 11 days ago by
Gordon Smyth
★ 7.2k • written 5 months ago by
raplayer
▴ 10
13
votes
14
replies
889
views
High Malat-1 expression in single cell data
single-cell
updated 7 days ago by
t.montserrat.ayuso
▴ 40 • written 16 days ago by
carolofharvest
▴ 40
2
votes
14
replies
2.9k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 1 day ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 12 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
10
votes
14
replies
737
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 8 days ago by
GenoMax
142k • written 14 days ago by
nicole.kavanagh
• 0
5
votes
13
replies
1.9k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 25 days ago by
ATpoint
82k • written 26 days ago by
BioinfGuru
★ 1.7k
4
votes
13
replies
1.0k
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 28 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
matteo.levorato
• 0
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 5 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 21 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 26 days ago by
Ram
43k • written 27 days ago by
iamsmor
• 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
28 days ago by
Ram
43k
9
votes
12
replies
4.2k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 28 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 27 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
4
votes
12
replies
4.9k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 6 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
16
votes
12
replies
7.4k
views
10 follow
how to split multi-fasta file into single fasta file named by header
genome
perl
python3
bash
python
updated 12 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 28 days ago by
Ram
43k • written 6.5 years ago by
shania90.lk
▴ 30
0
votes
11
replies
520
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
3 days ago by
Tuck898
• 0
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 22 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
4
votes
11
replies
874
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 21 days ago by
LauferVA
4.2k • written 22 days ago by
dominickd
• 0
0
votes
11
replies
704
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
19 days ago by
atowns21
• 0
23
votes
11
replies
4.9k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf
fasta
homopolymer
repeat
updated 29 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 19 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
2
votes
11
replies
989
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 16 days ago by
jkbonfield
★ 1.2k • written 28 days ago by
me
• 0
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 28 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
1
vote
11
replies
5.6k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 9 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
21 days ago by
DKA
▴ 40
2
votes
10
replies
3.5k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 28 days ago by
Ram
43k • written 7.5 years ago by
linda
• 0
7
votes
10
replies
2.8k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch
batch-effect
DESeq2
rna-seq
updated 28 days ago by
Ram
43k • written 2.1 years ago by
mmitra
▴ 60
0
votes
10
replies
605
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 15 days ago by
i.sudbery
19k • written 23 days ago by
Patadu94
• 0
9
votes
10
replies
4.5k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 28 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
9
votes
10
replies
7.0k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat
scRNA-seq
Harmony
RNA-seq
batch-effect
updated 27 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
3
votes
10
replies
690
views
Piping samtools to R
R
NGS
bash
samtools
28 days ago by
noodle
▴ 580
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma
microarray
DEA
batch-effect
updated 28 days ago by
Ram
43k • written 4.7 years ago by
asalimih
▴ 60
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 16 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
1
vote
10
replies
877
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 9 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
2
votes
9
replies
936
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 21 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
896 results • Page
1 of 18
Recent Votes
Answer: featureCounts output summary assigned value higher than uniquely mapped reads fr
Answer: Doubt about the process of annotation, detection, identification and classificat
Answer: Filtering VCF files based on VAF giving incorrect results
Problems with breakdancer (sv caller) output.
Problems with breakdancer (sv caller) output.
Comment: Add stats to boxplot in R
Answer: Genotyping sites with N in reference genome
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I know this was asked several years ago, but finding this post helped me solve my own problem and in the process I solved this one too. …
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by
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Thank you very much, you've helped me a lot
Comment: Filtering VCF files based on VAF giving incorrect results
by
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• 0
Thank you. I can't try a completely new tool but I will keep your command for future use. Do you think my commands were correct? For exampl…
Comment: Add stats to boxplot in R
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Thanks. Thats work
Comment: Genotyping sites with N in reference genome
by
Zhenyu Zhang
★ 1.2k
Whether N -> A/T/G/C represents a variant is heavily dependent on the tool itself, and I know most tools don't. Since you don't see it in y…
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marco.barr
▴ 110
The code seems correct at first glance... How did you generate the data in the Excel file? Have you checked the exon annotations? You could…
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142k
Did you remeber to unzip/untar the `nt` preformatted files that you downloaded?
Comment: Genotyping sites with N in reference genome
by
shpak.max
▴ 50
Just to clarify, I have set additional sites in the reference genome to 'N', which means (based on your statement) that these will not be g…
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
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Pierre Lindenbaum
161k
see https://www.biostars.org/p/9496674/ <!-- when i runed blastn(version 2.15) and nt database(latest version). I used aspera to download…
Answer: Genotyping sites with N in reference genome
by
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161k
> Does UnifiedGenotyper skip/ignore sites where the reference genotype is N yes. The variant is in YOUR data, not in the reference where '…
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Do you have samples that should in theory have a good degree over overlap in terms of cell types across the two sequencing types? I would …
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I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
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To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
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You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
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