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121,373 results • Page
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2
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9
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Different comparisons in RNASeq Analysis
DEGs
RNAseq
updated 4 hours ago by
swbarnes2
15k • written 11 hours ago by
SomeOne
▴ 200
0
votes
1
reply
84
views
Querying on non-canonical bacterial IDs
microbes
protein
accession
updated 7 hours ago by
Mensur Dlakic
★ 29k • written 8 hours ago by
benjamin.kellman
• 0
839
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
0
votes
2
replies
124
views
Distribution of assayed SNPs per sample
distribution
PLINK
missingness
updated 7 hours ago by
mbyvcm
▴ 460 • written 13 hours ago by
am29
▴ 60
0
votes
0
replies
69
views
News:
Learn Python for Biological Data Analysis – Online Course this September!
NGS
Python
Programming
15 hours ago by
Physalia-courses
★ 2.6k
3
votes
0
replies
105
views
Tutorial:
How to calculate partial correlation controlling cancer types
CRISPR
biology
correlation
computational
bioinformatics
1 day ago by
Ming Tommy Tang
★ 4.6k
0
votes
1
reply
127
views
SAIGE-GENE error
R
SAIGE
updated 1 day ago by
GenoMax
151k • written 1 day ago by
smyiz
▴ 30
2
votes
1
reply
346
views
IGV track display problem: interval rectangle from BED file appears above all tracks in white, overlapping each other
IGV
bed
1 day ago by
mcsimenc
▴ 30
2
votes
1
reply
163
views
Y-axis break in Volcano Plot
Volcano_Plot
Enhanced_Volcano
updated 1 day ago by
GenoMax
151k • written 1 day ago by
rajdeepboral00
▴ 70
1
vote
0
replies
113
views
How to rank a gene list using correlation coefficient and p-values for GSEA/clusterProfiler?
ClusterProfiler
GSEA
correlation
rank
genelist
1 day ago by
c-wes
▴ 10
2
votes
4
replies
298
views
Nanopore data analysis
nanopore
updated 1 day ago by
colindaven
7.6k • written 1 day ago by
sarahmanderni
▴ 130
6
votes
2
replies
1.4k
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 1 day ago by
ashotmarg2004
▴ 130 • written 21 months ago by
a615ebfb
▴ 50
0
votes
1
reply
152
views
checking the sequences that share origin
sequencing
updated 1 day ago by
GenoMax
151k • written 1 day ago by
QX
▴ 70
0
votes
0
replies
112
views
News:
Assembling Genomes with Oxford Nanopore: A Hands-On Guide to Long-Read Sequencing
Nanopore
GenomeAssembly
longreads
1 day ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
218
views
Bambu on illumina short reads sequencing
Bambu
updated 1 day ago by
Rob
7.1k • written 1 day ago by
Simone
• 0
0
votes
0
replies
125
views
Isoquant Major Exon Elongation
isoquant
nanopore
exon
2 days ago by
aico
• 0
0
votes
0
replies
130
views
bcftools run-roh error
roh
bcftools
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Pratiksha
• 0
0
votes
0
replies
142
views
News:
Workshop: Virtual Single-Cell Transcriptomics, June 24–26
Transcriptomics
workshop
UConn
2 days ago by
zsc25001
▴ 10
1
vote
6
replies
312
views
How can I find KO IDs for ORF sequences from kofam_scan ?
biology
Computational
Bioinformatics
2 days ago by
Nikesh
• 0
0
votes
0
replies
147
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
2 days ago by
Titus
▴ 910
4
votes
3
replies
300
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
1 day ago by
rajdeepboral00
▴ 70
0
votes
0
replies
132
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
2 days ago by
Pumla
• 0
1
vote
7
replies
382
views
Significant reads loss after fastp
fastp
loss
reads
updated 1 day ago by
GenoMax
151k • written 2 days ago by
SpliceAndScript
• 0
1
vote
1
reply
200
views
Shinyapps Server Down?
Shinyapps
Posit
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Arup Ghosh
3.3k
0
votes
2
replies
259
views
Data of microarray
Microarray
2 days ago by
Peter
• 0
0
votes
0
replies
172
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
2 days ago by
Minh-Anh
▴ 10
2
votes
4
replies
337
views
Best Tool for Fast RNA-Seq Transcriptome Alignment to Extract Unmapped Reads
mapping
rna-seq
2 days ago by
aeb
▴ 20
0
votes
2
replies
252
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
2 days ago by
SushiRoll
▴ 140
1
vote
2
replies
272
views
Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
3 days ago by
MitchT
▴ 10
4
votes
2
replies
261
views
Picard CollectRawWgsMetrics runs much slower on non-Apple chip machine
picard
updated 3 days ago by
Michael
55k • written 3 days ago by
adixon3
• 0
0
votes
0
replies
183
views
Reporting Imputed SNPs in GWAS
impute
GWAS
updated 3 days ago by
Ram
45k • written 3 days ago by
Aastha
• 0
0
votes
0
replies
161
views
Does Beagle use the reference genome for both phasing AND imputing genotypes?
beagle
genotypes
phasing
imputation
3 days ago by
giulia.trauzzi
▴ 30
0
votes
0
replies
163
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
3 days ago by
Begonia_pavonina
▴ 210
6
votes
2
replies
265
views
required annotations for VQSR
VQSR
vcf
annotation
3 days ago by
Mahdi&Christ
▴ 20
4
votes
4
replies
383
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
3 days ago by
ctmfarland
▴ 20
9
votes
9
replies
564
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
3 days ago by
KABILAN
▴ 130
0
votes
1
reply
248
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 3 days ago by
ATpoint
88k • written 4 days ago by
Yingying
▴ 10
0
votes
1
reply
766
views
Differential Expression tests for cell-type clusters from a single-cell RNAseq dataset with no biological replicates
cell-type
DEG
DE
single-cell
updated 4 days ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
2
votes
10
replies
546
views
Annotation Issue using miRBASE gff
NGS
miRNA
updated 3 days ago by
GenoMax
151k • written 4 days ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
200
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
4 days ago by
Claire Watson
▴ 60
1
vote
6
replies
388
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 3 days ago by
Michael
55k • written 4 days ago by
Bipin
▴ 10
4
votes
0
replies
226
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
4 days ago by
Anton
▴ 100
2
votes
0
replies
202
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
4 days ago by
Anton
▴ 100
2
votes
0
replies
217
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
4 days ago by
Anton
▴ 100
2
votes
0
replies
222
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
4 days ago by
Anton
▴ 100
0
votes
2
replies
262
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
4 days ago by
rbpdee
▴ 50
2
votes
7
replies
493
views
How to deal with intermediate files
procedures
data
operations
updated 4 days ago by
GenoMax
151k • written 5 days ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
240
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 4 days ago by
dthorbur
★ 3.0k • written 4 days ago by
Adrian
• 0
0
votes
1
reply
237
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Luwell
• 0
0
votes
1
reply
246
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 4 days ago by
patrickdm
▴ 260 • written 4 days ago by
adarsh
▴ 60
121,373 results • Page
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Answer: Batch correction in DESeq2
EdgeR without replicate?
Different comparisons in RNASeq Analysis
Different comparisons in RNASeq Analysis
Should I Run Clustering on PCA or t-SNE Components?
Public Electronic Health Records Database
Comment: RNA-seq analysis
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Recent Replies
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
You cannot remove batch effects where they overlap perfectly with a biological condition of interest.
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
That's not really the comparison OP was asking about, but I don't think they can meaningfully do the comparisons they wanted.
Comment: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
You will get slightly different alignment with longer paired reads. You don't want that if you want to compare the two sets of reads to ea…
Comment: Distribution of assayed SNPs per sample
by
mbyvcm
▴ 460
> According to my logic, one could do this by filtering out SNPs with missing genotype calls (./.), however when I did this, I ended up hav…
Answer: Different comparisons in RNASeq Analysis
by
mbyvcm
▴ 460
For analysis 3, you could think about something like: (Plant Mut vs. Plant WT) vs (Flask Mut vs. Flask WT) In doing so you are internally…
Answer: Querying on non-canonical bacterial IDs
by
Mensur Dlakic
★ 29k
I don't think there are any other records, including what you call canonical, for this protein. Maybe this will help you, using [**Entrez …
Comment: Different comparisons in RNASeq Analysis
by
jkim
▴ 190
See [the post](https://www.biostars.org/p/403053/#473727).
Comment: Different comparisons in RNASeq Analysis
by
SomeOne
▴ 200
Hi. Thank you for replying. If i trim the PE data to SE and at 75bp length, and perform the analysis. Wouldn’t that effect the final co…
Comment: Different comparisons in RNASeq Analysis
by
SomeOne
▴ 200
Hi! Thank you for your response. Can you share some information on how to remove this batch effect ?
Answer: Different comparisons in RNASeq Analysis
by
swbarnes2
15k
> or the Different sequence-type (paired vs single), difference in > read-length (150bp-x2 vs 75bp-x1) will have any technical or batch …
Comment: Different comparisons in RNASeq Analysis
by
jkim
▴ 190
For analyses 3 and 4, you will need to account for batch effects, which I expect to be substantial given the differences between datasets—e…
Comment: Distribution of assayed SNPs per sample
by
1769mkc
★ 1.3k
if you can share some part of the data that would be helpful what you are trying and what the final output expected , that helps for people…
Comment: Trouble building combined pangenome graph with circularized genomes + embedded O
by
Jordan M Eizenga
▴ 740
That error is caused by a simple failure to open that file (which is created in the `vg prune`). Usually, that results from a typo in the f…
Comment: SAIGE-GENE error
by
GenoMax
151k
Segfaults are related to memory, which is what part of the message is telling you. If you are running this job under a job scheduler make s…
Answer: IGV track display problem: interval rectangle from BED file appears above all tr
by
mcsimenc
▴ 30
The problem was the filename suffix, it's meaningful in how IGV treats the file. It is .pk here, but changed to .bed and it works.
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