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882 results • Page
1 of 18
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Votes
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76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
16 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 24 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 9 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 23 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
38
votes
24
replies
2.1k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq
STAR
NGS
Illumina
updated 11 days ago by
i.sudbery
19k • written 14 days ago by
noodle
▴ 580
9
votes
23
replies
9.8k
views
Tool:
BioLabDonkey - new Mac program for molecular biologists
software
biolabdonkey
9 hours ago by
vytarasov
▴ 180
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 24 days ago by
Ram
43k • written 5.3 years ago by
iraia.munoa
▴ 130
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 24 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 23 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 24 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 22 days ago by
Hagen
▴ 10 • written 10.3 years ago by
filipzembol
▴ 180
8
votes
16
replies
1.1k
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 15 days ago by
bk11
★ 2.4k • written 9 weeks ago by
Sofia
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 4 days ago by
Pierre Lindenbaum
161k • written 5.8 years ago by
mostafarafiepour
▴ 180
0
votes
16
replies
1.1k
views
What is the sequence origin in human plasma?
human
sequence
cfDNA
28 days ago by
biwdpang
• 0
7
votes
16
replies
805
views
How many reads for WGS Sequencing?
WGS
Bacterial-Genomics
12 days ago by
Ruqaiya
• 0
4
votes
15
replies
1.6k
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 7 days ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
13
votes
14
replies
831
views
High Malat-1 expression in single cell data
single-cell
updated 3 days ago by
t.montserrat.ayuso
▴ 40 • written 12 days ago by
carolofharvest
▴ 40
10
votes
14
replies
681
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 4 days ago by
GenoMax
142k • written 10 days ago by
nicole.kavanagh
• 0
1
vote
14
replies
2.4k
views
Extract gRNA sequence using cutadapt
cutadapt
trimming
crispr
sequencing
updated 9 days ago by
GenoMax
142k • written 4.5 years ago by
Swimming bird
▴ 20
9
votes
13
replies
4.8k
views
Custom Reference panel creation for data imputation from .vcf files
imputation
reference panel
updated 1 day ago by
analyst
▴ 50 • written 6.4 years ago by
David_emir
▴ 490
4
votes
13
replies
978
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 24 days ago by
BioinfGuru
★ 1.7k • written 4 weeks ago by
matteo.levorato
• 0
0
votes
13
replies
3.6k
views
6 follow
Tax4Fun2 - error
tax4fun
silva
blast
updated 17 days ago by
drstalinantony28
• 0 • written 2.2 years ago by
ymj
▴ 10
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 21 days ago by
ATpoint
82k • written 22 days ago by
BioinfGuru
★ 1.7k
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression
TPM
RNA-Seq
counts
batch-effect
24 days ago by
Ram
43k
2
votes
12
replies
2.7k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 3 days ago by
Anitha
• 0 • written 4.8 years ago by
ww22runner
▴ 60
11
votes
12
replies
1.1k
views
Downloaded pdb's on rcsb.org
rcsb
pdb
updated 22 days ago by
Ram
43k • written 23 days ago by
iamsmor
• 0
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq
deseq2
batch-effect
updated 24 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 23 days ago by
kjngo
• 0 • written 12.1 years ago by
Gabriel R.
★ 2.9k
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 8 days ago by
rsieber
▴ 10 • written 3.1 years ago by
Kumar
▴ 120
30
votes
12
replies
3.9k
views
Trying to understand the maths behind one Limma function
limma
RNA-Seq
batch-effect
updated 26 days ago by
Ram
43k • written 4.0 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 2 days ago by
Tawny
▴ 180 • written 3.0 years ago by
julia_geh
▴ 20
2
votes
11
replies
962
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 12 days ago by
jkbonfield
★ 1.2k • written 24 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 25 days ago by
Ram
43k • written 5.0 years ago by
WouterDeCoster
47k
4
votes
11
replies
853
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 17 days ago by
LauferVA
4.2k • written 18 days ago by
dominickd
• 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 15 days ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
6
votes
11
replies
3.4k
views
Collapsing probesets to genes on WGCNA
WGCNA
gene-expression
R
updated 24 days ago by
Ram
43k • written 5.3 years ago by
Davide Chicco
▴ 120
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
15 days ago by
atowns21
• 0
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 5 days ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
25
votes
11
replies
3.8k
views
6 follow
Forum:
Site Use Guidelines
meta
biostars
Guidelines
updated 18 days ago by
Ram
43k • written 14.6 years ago by
Istvan Albert
100k
3
votes
11
replies
6.0k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 24 days ago by
Ram
43k • written 6.5 years ago by
shania90.lk
▴ 30
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 24 days ago by
Ram
43k • written 7.4 years ago by
linda
• 0
40
votes
10
replies
42k
views
8 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma
sva
Combat
batch-effect
updated 12 days ago by
cwwong13
▴ 40 • written 6.8 years ago by
lessismore
★ 1.3k
9
votes
10
replies
4.5k
views
Using rnaseq reference sample across batches
RNA-Seq
batch-effect
updated 24 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 23 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
17 days ago by
DKA
▴ 40
8
votes
10
replies
795
views
bash script
whole-genome-sequencing
updated 26 days ago by
Ram
43k • written 4 weeks ago by
bestone
▴ 30
1
vote
10
replies
4.0k
views
Error in CIBERSORTx
RNA-seq
CIBERSORT
LM22
updated 27 days ago by
Aspire
▴ 330 • written 19 months ago by
Manav
• 0
1
vote
10
replies
864
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 5 days ago by
antonio.spl
• 0 • written 4 months ago by
microorganism_001
▴ 30
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 25 days ago by
Ram
43k • written 2.1 years ago by
mmitra
▴ 60
0
votes
10
replies
575
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 11 days ago by
i.sudbery
19k • written 19 days ago by
Patadu94
• 0
882 results • Page
1 of 18
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Answer: install package
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
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Answer: Kraken2 database
by
Mathew
▴ 60
Sorry, what analysis are you trying to perform with these databases? Based on your question, it appears you are using Kraken2 and Bracken.…
Comment: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
Mathew
▴ 60
I looked up a publication using CIBERSORT to see how they got the package, and indeed they acquired it through official website application…
Comment: Adata.raw.X in LIANA, something wrong with conversion from Seurat to adata in py
by
fracarb8
★ 1.6k
If you are using R, you should check the liana R implementation (https://github.com/saezlab/liana).
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thank you Pierre, I am going to take some time to get my head around this and report back if it works.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
ajbarrett98
• 0
Thanks for the crosspost! Just trying to get things figured out.
Answer: error in fun(x((i)), ...) : only defined on a data frame with all numeric alike
by
ATpoint
82k
To the best of my knowledge, CIBERSORT is and has always and only been available via the official website application from Stanford. Whatev…
Comment: BioLabDonkey - new Mac program for molecular biologists
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▴ 180
Update of BioLabDonkey - Version 5.6 - In silico PCR function is added.
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File
by
Pierre Lindenbaum
161k
cross posted: https://stackoverflow.com/questions/78462732/ > Please mind that posting the same question to multiple sites can be perceive…
Comment: java.nio.bufferunderflowexception haplotypecaller error for bqsr reads
by
Pierre Lindenbaum
161k
command is missing, version is missing.
Answer: Failed to open VCF file
by
Pierre Lindenbaum
161k
> Error: Failed to open vcf file Fixing: No such file or directory one of your file is missing, obviously. Check files exist using `[…
Comment: Align paired and unpaired reads simultaneously using Bowtie2?
by
Ruqaiya
• 0
I have forward reads that didn't require any trimming except for adapter sequence. but the reverse read file required trimming so i trimmed…
Comment: Trimmomatic: What is the difference between paired and unpaired output files in
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Ruqaiya
• 0
can we not mention unpaired ? i have a reverse read file that needs a lot of trimming but forward file is usable. I don't understand how to…
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rackbersingh
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It is an indeed an old assignment question, I am doing revision and practicing answering questions for an upcoming test and just wanted to …
Comment: How are score_weights calculated in this code?
by
carolofharvest
▴ 40
I've found this code [in this site :][1] . It doesn't seem like they've shared any additional information about this in the previous line…
Comment: Correlation Analysis
by
Researcher
▴ 30
Thank you so much. I ran based on the above code and found that all gene columns have the same values, which you obtain as the average corr…
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