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869 results • Page
1 of 18
Sort: replies
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Views
Votes
Replies
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
18 days ago by
Kevin Blighe
87k
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 26 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 10 days ago by
thomas.heigl.ibk
• 0 • written 12.8 years ago by
Bioscientist
★ 1.7k
38
votes
24
replies
2.1k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 12 days ago by
i.sudbery
19k • written 15 days ago by
noodle
▴ 580
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 25 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
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 25 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
1 day 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 26 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 24 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 26 days ago by
Ram
43k • written 9.6 years ago by
james.lloyd
▴ 100
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read
length
bam
updated 23 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 5 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 16 days ago by
bk11
★ 2.4k • written 9 weeks ago by
Sofia
• 0
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
29 days ago by
biwdpang
• 0
7
votes
16
replies
835
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
13 days ago by
Ruqaiya
• 0
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 9 days ago by
Gordon Smyth
★ 7.1k • written 5 months ago by
raplayer
▴ 10
13
votes
14
replies
841
views
High Malat-1 expression in single cell data
single-cell
updated 5 days ago by
t.montserrat.ayuso
▴ 40 • written 13 days ago by
carolofharvest
▴ 40
10
votes
14
replies
683
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 5 days ago by
GenoMax
142k • written 11 days ago by
nicole.kavanagh
• 0
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 10 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
5
votes
13
replies
1.8k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 22 days ago by
ATpoint
82k • written 23 days ago by
BioinfGuru
★ 1.7k
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 18 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 2 days ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
2
votes
13
replies
2.8k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 38 minutes ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
4
votes
13
replies
984
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 26 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
matteo.levorato
• 0
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
25 days ago by
Ram
43k
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 25 days ago by
Ram
43k • written 5.0 years ago by
Mozart
▴ 330
4
votes
12
replies
4.8k
views
10 follow
How to analyze Infinium Mouse Methylation BeadChip array data?
Methylation
Experience
Illumina
Mouse
updated 3 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 9 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 24 days ago by
Ram
43k • written 24 days ago by
iamsmor
• 0
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 27 days ago by
Ram
43k • written 4.0 years ago by
Mozart
▴ 330
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 24 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
0
votes
11
replies
683
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
17 days ago by
atowns21
• 0
4
votes
11
replies
857
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 19 days ago by
LauferVA
4.2k • written 20 days ago by
dominickd
• 0
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 19 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
0
votes
11
replies
430
views
In IGV is this a heterogeneous mutation or false call?
mutations
IGV
heterogeneous
11 hours ago by
Tuck898
• 0
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 16 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 7 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 26 days ago by
Ram
43k • written 6.5 years ago by
shania90.lk
▴ 30
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 26 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
2
votes
11
replies
965
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 13 days ago by
jkbonfield
★ 1.2k • written 25 days ago by
me
• 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 26 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
9
votes
10
replies
4.5k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 26 days ago by
Ram
43k • written 7.4 years ago by
denalitastic
▴ 30
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 13 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
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 24 days ago by
Ram
43k • written 4.6 years ago by
Lucy
▴ 140
1
vote
10
replies
1.0k
views
Troubleshooting RNA-seq data with DNA contamination
RNA-seq
DESeq2
DNA-contamination
18 days ago by
DKA
▴ 40
0
votes
10
replies
577
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 12 days ago by
i.sudbery
19k • written 20 days ago by
Patadu94
• 0
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 28 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
1
vote
10
replies
868
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 7 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
3
votes
10
replies
685
views
Piping samtools to R
R
NGS
bash
samtools
26 days ago by
noodle
▴ 580
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 26 days ago by
Ram
43k • written 7.5 years ago by
linda
• 0
869 results • Page
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Recent Votes
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Answer: CNVKIT - unable to produce scatter and diagram pdfs
by
Anitha
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While running with this batch option batch --method wgs option. I have used this command " cnvkit.py batch tumor.bam -n normal.bam -m wgs -…
Answer: Generating .bed file and .map file for polyploid vcf file through plink
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10k
Why do you think ADMIXTURE supports polyploid input? (Note that this is an answer, not a comment.)
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feather-W
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Hi ATpoint, Thanks for your reply!
Comment: How to convert normalized BigWig file to count matrix?
by
feather-W
• 0
Hi Pierre, Thanks for your reply! I want to get a feature count matrix from coverage data stored in BigWig files. And this BigWig file ha…
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you can assume all genes without mutation is WT (easy) while controlling for (difficult) - coverage - capture region - germline - the …
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Since you are getting data from the GDC, analysis-related reference/annotations can be found in the GDC reference page here https://gdc.can…
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I saw that, but considering that your analysis is in seurat and that both liana and liana+ are from the same developers, it might be quicke…
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You can rank normalize them, but to tell the truth, I won't trust any conclusion you can draw from such combined data. The recommended …
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by
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82k
Include confounders into the limma design. No need for upfront removal. Note that libsize is taken care of by normalizing usually. Are you …
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sansan_96
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Thank you very much, success in your projects.
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by
Tuck898
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Thanks for the input :)
Comment: install package: package ‘gmwm’ is not available for this version of R
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This seems to indicate that the package itself (or packages it depends on) are not compatible with the R version you are using. Next step c…
Answer: Tissue-specific DEG analysis with DEseq2
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arctic
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Not my area of expertise but GTEx portal seems to offer visual comparison of expression across tissues, maybe checking their pipeline could…
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by
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161k
> I think I am mostly struggling with what would need to be coded to my dataset here and how to run this loop on my set in general. i do…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Pierre, I am a novice at all of this in general and I have never used Java-based programming before. I may not be able to properly wrangl…
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