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1,000 results • Page
5 of 20
Sort: Votes
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Views
Votes
Replies
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression
Salmon
updated 16 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
3
votes
7
replies
961
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 21 days ago by
Ram
43k • written 5 months ago by
bioinfo
▴ 150
3
votes
2
replies
511
views
Fail to install umap-learn in R
cellchat
R
updated 22 days ago by
Ram
43k • written 8 weeks ago by
synat.keam
▴ 100
3
votes
16
replies
2.7k
views
design matrix for dge
limma
differential-gene-expression
r
updated 16 days ago by
Ram
43k • written 7.9 years ago by
1234anjalianjali1234
▴ 50
3
votes
4
replies
353
views
Single cell analysis with "meta".tsv.gz file
Single-cell
23 days ago by
Estevão
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 8 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR
differential-gene-expression
edgeR
miRNA
updated 16 days ago by
Ram
43k • written 4.9 years ago by
AngAdd
▴ 20
3
votes
3
replies
334
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
14 days ago by
george
• 0
3
votes
6
replies
11k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 9 days ago by
Bioinfotec
▴ 10 • written 7.6 years ago by
nut_B
▴ 10
3
votes
1
reply
268
views
ClueGO is not showing custom data
ClueGo
Cytoscape
updated 15 days ago by
Scooter
▴ 280 • written 21 days ago by
Nicolas
• 0
3
votes
8
replies
496
views
PCA plot (Suggestions Needed)
DESeq2
PCAplot
updated 1 day ago by
swbarnes2
14k • written 2 days ago by
Aaliya
▴ 10
3
votes
3
replies
776
views
GATK error on HPC clusters
variant-calling
SNP
updated 23 days ago by
Ram
43k • written 12 months ago by
princy149
• 0
3
votes
5
replies
261
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 3 days ago by
GenoMax
141k • written 4 days ago by
ahmad.sajad4541
• 0
3
votes
6
replies
892
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
3
votes
7
replies
458
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
9 days ago by
ntsopoul
▴ 60
3
votes
2
replies
565
views
News:
Announcement: Research Topic "Mechanistic, Machine Learning and Hybrid Models of the 'Other' Endocrine Regulatory Systems in Health and Disease", Vol…
mathematical-modelling
endocrinology
ML
systems-biology
machine-learning
27 days ago by
Johannes W. Dietrich
• 0
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 9 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
3
votes
3
replies
167
views
Sequence read length shorter than flow cell specification
illumina
NGS
sequencing
updated 13 hours ago by
swbarnes2
14k • written 19 hours ago by
M
• 0
3
votes
3
replies
191
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
c_u
▴ 520
3
votes
5
replies
1.4k
views
Removing Batch effect that is the same as condition - DESEq2
RNA-Seq
batch-effect
DESeq2
updated 17 days ago by
Ram
43k • written 3.9 years ago by
annamariabugaj
• 0
3
votes
0
replies
112
views
News:
Interested in Spatial Omics?
Bioconductor
Spatial-Omics
Spatial-Transcriptomics
updated 2 days ago by
Ram
43k • written 2 days ago by
carlopecoraro2
★ 2.5k
3
votes
7
replies
518
views
Artificial deletion in bam
bam
updated 20 days ago by
Zhenyu Zhang
★ 1.2k • written 21 days ago by
enee
▴ 10
3
votes
2
replies
339
views
FDR and Bonferroni
FDR
Bonferroni
updated 29 days ago by
joe
▴ 510 • written 4 weeks ago by
song
• 0
3
votes
9
replies
791
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 7 days ago by
Elisabeth Gasteiger
★ 2.4k • written 8 days ago by
Jacky
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 7 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
1
reply
210
views
Seurat merge and batch correction
Seurat
updated 2 days ago by
Ram
43k • written 3 days ago by
sooni
▴ 20
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 9 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
4
replies
225
views
Why gatk VariantAnnotator required bam and coverage files
gatk
VariantAnnotator
16 hours ago by
QX
• 0
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
3
votes
1
reply
162
views
NCBI CLI Download all proteins from Taxid
ncbi
updated 23 days ago by
GenoMax
141k • written 24 days ago by
dthorbur
★ 1.9k
3
votes
3
replies
624
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression
TCGA
miRNA
updated 16 days ago by
Ram
43k • written 5 months ago by
mohammadhassanj
▴ 260
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 7 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
1
reply
264
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 14 days ago by
Ram
43k • written 14 days ago by
rj.rezwan
• 0
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 7 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 9 days ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
3
votes
4
replies
388
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness
contamination
21 days ago by
beacamara
• 0
3
votes
2
replies
240
views
Gene reads all zero for each sample
R
salmon
DE
DESeq2
28 days ago by
DYLAN NICO
• 0
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 7 days ago by
Ram
43k • written 4.6 years ago by
hkarakurt
▴ 180
3
votes
10
replies
8.5k
views
6 follow
GATK HaolotypeCaller takes too much time for variant calling
HaplotypeCaller
GATK
updated 20 days ago by
Ram
43k • written 6.4 years ago by
J.F.Jiang
▴ 920
3
votes
1
reply
870
views
Fisher exact test in R package
Fisher-test
updated 23 days ago by
Ram
43k • written 2.9 years ago by
Nuglozeh
▴ 10
3
votes
10
replies
602
views
Piping samtools to R
R
NGS
bash
samtools
9 days ago by
joe
▴ 510
3
votes
2
replies
332
views
kraken2 vs krakenuniq
KrakenUniq
kraken2
20 days ago by
pinheirofabiano
▴ 10
3
votes
2
replies
231
views
Interproscan taking so much time
slurm
interproscan
transcriptomics
updated 29 days ago by
dthorbur
★ 1.9k • written 29 days ago by
Mohamed Abderrahmane
▴ 20
3
votes
2
replies
812
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 9 days ago by
Ram
43k • written 3.2 years ago by
helia.ziaei
• 0
3
votes
3
replies
469
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 6 days ago by
swbarnes2
14k • written 7 days ago by
joe
▴ 510
3
votes
0
replies
154
views
Herald:
The Biostar Herald for Tuesday, April 09, 2024
herald
16 days ago by
Biostar
2.7k
3
votes
3
replies
287
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 9 days ago by
GenoMax
141k • written 9 days ago by
lorena9132
• 0
3
votes
3
replies
215
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Estevão
• 0
3
votes
3
replies
501
views
Korean human genome reference file
GWAS
reference
imputation
7 days ago by
SeoGyun
• 0
1,000 results • Page
5 of 20
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How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
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Comment: what is the purpose of indexing the reference genome (Kallisto)
by
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19k
Specifically: If we want to look up all the places where a 31mer is in a genome without and index, we have to compare that 31 to the first…
Answer: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
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3.9k
This is way easier to do solely in R now 10 years later. library(GenomicFeatures) library(rtracklayer) ## import GTF…
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Thank you for replying Pierre. I first added a third column to the SNP bed file, so that I would get a range of 1 for each SNP awk 'B…
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> using bcftools Show us what you tried
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These are the first lines of the output: (Please is it normal to have NA in the P value column ?) CHR …
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