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110,548 results • Page
1 of 2211
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Using Tumor Immune Dysfunction and Exclusion (TIDE)
prediction
TPM
cancer
normalization
r
12 minutes ago by
JACKY
▴ 100
0
votes
0
replies
13
views
question related to novel mirna file from miRDeep2?
miRDeep2
48 minutes ago by
kuttibiotech2009
▴ 30
0
votes
1
reply
48
views
Do rna SRA files contain introns ?
RNA-seq
SRA
updated 31 minutes ago by
Ram
39k • written 2 hours ago by
firefox91
• 0
0
votes
0
replies
42
views
synteny viewer
genomics
comparative
synteny
3 hours ago by
shwetamgr1
▴ 10
0
votes
0
replies
34
views
How to create a haplotype map?
exomes
CrosscheckFingerprints
haplotype
picard
swapping
3 hours ago by
jgarces
▴ 30
0
votes
2
replies
80
views
Blast reads classification
blast
tabular
NGS
magicblast
reads
updated 2 hours ago by
GenoMax
130k • written 3 hours ago by
Giulia.cosenza
▴ 80
744
votes
162
replies
114k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
1
vote
0
replies
64
views
News:
Good bioinformatics training resources
NGS
updated 4 hours ago by
Pierre Lindenbaum
154k • written 5 hours ago by
ManuelDB
▴ 40
1
vote
4
replies
107
views
Normalized counts bulk RNA-seq to DEGs
RNA-seq
updated 1 hour ago by
ATpoint
72k • written 4 hours ago by
t.ru
▴ 20
0
votes
2
replies
93
views
Reorder GO terms using R
enrichment-analysis
GO
updated 33 minutes ago by
Ram
39k • written 7 hours ago by
hellokwmin
• 0
0
votes
0
replies
32
views
Required input files for COHCAP
TCGA
Methylation
input
COHCAP
5 hours ago by
dilrajkaur766
• 0
0
votes
3
replies
91
views
motis SSR
SSR
motis
updated 1 hour ago by
Jesse
▴ 580 • written 7 hours ago by
m.esmaeilpour
▴ 10
0
votes
2
replies
80
views
Chain file for Homo_sapiens_assembly38.fasta to liftover Nebula vcf
hg38
fasta
hg19
chainfile
4 hours ago by
berndmann
▴ 10
0
votes
0
replies
41
views
Forum:
Recommendation sought for differential exon usage of a single gene
splicing
differential-exon-usage
updated 30 minutes ago by
Ram
39k • written 6 hours ago by
nick_brittain55
▴ 10
0
votes
1
reply
72
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly
removal
bacterial
genome
vector
updated 2 hours ago by
GenoMax
130k • written 7 hours ago by
mathavanbioinfo
▴ 70
0
votes
1
reply
100
views
How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?
differential-expression
TPM
GSEA
PANDA
updated 50 minutes ago by
Ram
39k • written 8 hours ago by
John
• 0
0
votes
1
reply
75
views
Appropriate RPKM cutoff
RNA-Seq
Sequencing
updated 3 hours ago by
dsull
★ 4.2k • written 8 hours ago by
Lilla
• 0
1
vote
1
reply
79
views
Plotting GO enrichment DATA
R
GO
enrichment-analysis
updated 30 minutes ago by
Ram
39k • written 8 hours ago by
hellokwmin
• 0
0
votes
0
replies
48
views
Popcorn using SNPs with extremely low P-value
Popcorn
SNP
9 hours ago by
Apprentice
▴ 140
0
votes
1
reply
1.8k
views
Adjusting for batch effect and covariates with ComBat
batch-effect
RNA-Seq
combat
updated 40 minutes ago by
Ram
39k • written 2.6 years ago by
juara
▴ 40
0
votes
1
reply
106
views
UCSC genome browser
Genome-browser
shannon-entropy
updated 50 minutes ago by
Ram
39k • written 14 hours ago by
Lkhagvadulam
• 0
0
votes
0
replies
53
views
CIBERSORTx hires mode duplicates
CIBERSORT
CIBERSORTx
RNA-seq
bulk
deconvolution
15 hours ago by
michaelhojungyoon
• 0
1
vote
1
reply
86
views
plyranges:: summarise() not recognizing previous summarized column (counts)
cpg
R
plyranges
14 hours ago by
Alewa
▴ 120
0
votes
0
replies
73
views
Copy Number Alteration and Loss or Heterozygosity
LOH
CNA
copy-number
updated 30 minutes ago by
Ram
39k • written 17 hours ago by
Bogdan
★ 1.3k
1
vote
4
replies
158
views
How to get information about promoter from bulk-RNAseq?
promoter
R
RNA-seq
17 hours ago by
camillab.
▴ 130
0
votes
1
reply
106
views
How to add annotation columns with specific colors to the heatmap?
R
heatmap
RNA-seq
updated 30 minutes ago by
Ram
39k • written 18 hours ago by
ahmad mousavi
▴ 750
3
votes
5
replies
201
views
Differences in GTF files hg19 and hg38
hg38
hg19
GTF
12 hours ago by
heureuse
• 0
0
votes
3
replies
123
views
CellRanger problem
RNA-seq
STAR
scRNA
updated 18 hours ago by
Arup Ghosh
3.2k • written 19 hours ago by
Carlos Eduardo
• 0
0
votes
5
replies
171
views
VCF file CSQ flag
vcf
exome-sequencing
updated 18 hours ago by
Ram
39k • written 19 hours ago by
Payal
▴ 140
3
votes
1
reply
95
views
Saving results from yeastgenome.org blastp search
blast
blastp
updated 20 hours ago by
GenoMax
130k • written 21 hours ago by
dec986
▴ 360
0
votes
0
replies
67
views
normalize for sample size in single cell rna seq cluster frequencies data
scRNAseq
seurat
10x
23 hours ago by
chi.delta
▴ 40
2
votes
3
replies
205
views
counts matrix should be numeric, currently it has mode: character when using a csv file in R for DESeq2
DESeq2
updated 21 hours ago by
Ram
39k • written 1 day ago by
Sara
▴ 220
0
votes
2
replies
106
views
sgRNA design
gene-editing
1 hour ago by
elisa.qinxue
• 0
1
vote
1
reply
95
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 23 hours ago by
GenoMax
130k • written 1 day ago by
saint-even
• 0
0
votes
0
replies
61
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
1 day ago by
dilrajkaur766
• 0
0
votes
0
replies
65
views
m6A-seq input normalisation with RNA-seq
m6A-seq
MeRIP-Seq
normalisation
deepTools
updated 1 day ago by
Ram
39k • written 1 day ago by
Parichitran
• 0
0
votes
1
reply
120
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 21 hours ago by
Ram
39k • written 1 day ago by
aaronlogsdon2001
• 0
16
votes
8
replies
379
views
Tool:
ChatGPT optimized for bioinformatics questions
gpt
22 hours ago by
Sasha
▴ 280
2
votes
4
replies
338
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 15 hours ago by
Rory Stark
★ 1.8k • written 2 days ago by
B.N.
• 0
2
votes
3
replies
283
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
22 hours ago by
B.N.
• 0
0
votes
0
replies
61
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
1 day ago by
cate.cevallos
• 0
1
vote
4
replies
193
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 23 hours ago by
ATpoint
72k • written 1 day ago by
Zhichao
• 0
0
votes
1
reply
94
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 1 day ago by
ATpoint
72k • written 1 day ago by
f2ff7a46
• 0
0
votes
1
reply
118
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 1 day ago by
ATpoint
72k • written 1 day ago by
t.ru
▴ 20
0
votes
2
replies
130
views
Visualizing several genomes/plasmids in a single figure
visualization
8 hours ago by
blur
▴ 270
1
vote
1
reply
107
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 1 day ago by
GenoMax
130k • written 1 day ago by
lait
▴ 170
4
votes
17
replies
665
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
2 hours ago by
melissachua90
▴ 40
4
votes
8
replies
290
views
Extract sequences from a fastq file by a list of IDs
fastq
updated 20 hours ago by
Ram
39k • written 1 day ago by
mhpakdel96
▴ 10
0
votes
0
replies
57
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
1 day ago by
Sapphire
• 0
0
votes
0
replies
81
views
Complex Phylogenetic Tree Annotation
annotation
protein
phylogenetic-tree
updated 1 day ago by
Ram
39k • written 1 day ago by
Aanushka
• 0
110,548 results • Page
1 of 2211
Recent Votes
Good bioinformatics training resources
A: VCF files: Change Chromosome Notation
Answer: Add NES value to GSEA plot
Plotting GSEA output in R
Answer: Haplotype map Picard CrosscheckFingerprints
Can the code of a R package be changed? How?
How to calculate the similairty of two protein structures in .pdb file format or how to measure the accuracy of alphafold predicted protein structure?
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▴ 140
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GenoMax
130k
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Recent Replies
Comment: Does adding reads cause batch effects?
by
bioinfo
▴ 80
Would the number of reads in each batch affect the PCA? I do notice some batch effect. For example, I have one batch where most samples hav…
Comment: Error occured at the PHG imputation step: allele in genotype not in the variant
by
lcj34
▴ 230
We are aware of this problem and are trying to diagnose. I will post here when we have a solution and a new build.
Comment: sgRNA design
by
elisa.qinxue
• 0
So it would be OK no matter where I would like to cut if I use appropriate sgRNA, like below. ![enter image description here][1] [1]: …
Comment: Normalized counts bulk RNA-seq to DEGs
by
ATpoint
72k
Then ask for raw counts. Analysis is anyway not reproducible and hence not publishable without the raw data at hand.
Comment: Normalized counts bulk RNA-seq to DEGs
by
t.ru
▴ 20
I only have output as normalized counts. I did not do that part.
Comment: motis SSR
by
Jesse
▴ 580
What does the LLM's reply mean by "the sequences provided are aligned"?
Comment: How to use Rfam annotate small RNA and how to see differential expression of nov
by
kuttibiotech2009
▴ 30
I am also facing the same issues. Can you please tell me how to do this using bedtools?
Answer: Do rna SRA files contain introns ?
by
i.sudbery
17k
SRA contains all sorts of data, and what is contained in an SRA file will depend entirely on what data was put into it by the submitter. …
Comment: Blast reads classification
by
GenoMax
130k
Your input file names seem to indicate these data are quality filtered, scanned and trimmed reads. If that was not the case I would have su…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
1. My expression data is raw RNA-seq counts 2. I'm testing the differential expression across all the groups I added my dput
Comment: How to remove cloning vector sequence from bacterial assembled genome?
by
GenoMax
130k
You could use an alignment program and vector reference to identify the vector (if it was assembled as a single piece in your data). Idea…
Comment: Blast reads classification
by
lieven.sterck
14k
couple of things: * BLAST: basic LOCAL alignment search tool , hence it only does local alignments and will as such report the best hit, w…
Comment: filtering sniffles variants for precise calls
by
Edward E-B
• 0
For some reason I couldn't post the different options I had tried but I did try using bcftools view -i/e in different ways but could not ge…
Answer: Appropriate RPKM cutoff
by
dsull
★ 4.2k
There is no good "cutoff" for what is "expressed" (and even the word "expressed" is kind of vague -- if a read mapping perfectly+unambiguou…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
I am out here. You are ignoring the recommendations given to you so it's a waste of time. Read my lenghty comment and the answers again, or…
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