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179 results • Page
2 of 4
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Views
Votes
Replies
1
vote
5
replies
329
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
3 days ago by
Riccardo
▴ 10
3
votes
3
replies
324
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 6 days ago by
noodle
▴ 580 • written 7 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
322
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 1 day ago by
GenoMax
142k • written 1 day ago by
tulip
• 0
3
votes
3
replies
321
views
What analysis suitable to identify similarly expressed genes between two samples (treated vs untreated). Contrary to DGE analysis,
Gene-Expression
RNA
NOISeq
DGE
updated 3 days ago by
ATpoint
82k • written 4 days ago by
alifafiq1
• 0
0
votes
5
replies
316
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 2 days ago by
chrchang523
10k • written 3 days ago by
curious
▴ 750
0
votes
5
replies
311
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 3 days ago by
Mohamed Abderrahmane
▴ 20 • written 7 days ago by
matteo.levorato
• 0
3
votes
5
replies
310
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
2 days ago by
Maverick
▴ 10
4
votes
2
replies
307
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
6 days ago by
pairedttest
▴ 10
1
vote
3
replies
307
views
DESeq2 processing problems
deseq2
R
updated 4 days ago by
ATpoint
82k • written 5 days ago by
jagdish7921
• 0
1
vote
4
replies
306
views
Segmentation error while using a tool
smalt
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Ruqaiya
• 0
2
votes
4
replies
294
views
from row count to tpm
tpm
row-count
normalization
updated 6 days ago by
Ram
43k • written 14 days ago by
michelafrancesconi9
▴ 20
0
votes
3
replies
294
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 6 days ago by
GenoMax
142k • written 6 days ago by
kim
• 0
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
5 days ago by
Nafi
• 0
0
votes
6
replies
290
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 3 days ago by
dsull
★ 6.0k • written 4 days ago by
Chen
• 0
0
votes
1
reply
289
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
6 days ago by
David Langenberger
11k
1
vote
5
replies
287
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 2 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
3
replies
285
views
KEGG Pathways
r
RNA-seq
updated 5 days ago by
Ram
43k • written 6 days ago by
Sudip
• 0
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 6 days ago by
Lluís R.
★ 1.2k • written 6 days ago by
이민경[학생](대학원 융합의과학과)
• 0
1
vote
2
replies
280
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
3 days ago by
eebloom
▴ 80
1
vote
3
replies
280
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 5 days ago by
GenoMax
142k • written 6 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
280
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 3 days ago by
ATpoint
82k • written 3 days ago by
Qi
• 0
1
vote
3
replies
278
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
11 hours ago by
Dora
▴ 10
5
votes
5
replies
275
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 4 days ago by
atharvakarkare14
▴ 30 • written 4 days ago by
Begonia_pavonina
▴ 150
0
votes
4
replies
275
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 6 days ago by
Ram
43k • written 6 days ago by
Hamtaro
▴ 50
0
votes
1
reply
275
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 4 days ago by
Scooter
▴ 280 • written 10 days ago by
avocado123
• 0
2
votes
2
replies
274
views
p-value in CIBERSORT
CIBERSORT
p-value
5 days ago by
michelafrancesconi9
▴ 20
2
votes
3
replies
273
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 3 days ago by
dthorbur
★ 1.9k • written 3 days ago by
Vijith
▴ 30
2
votes
2
replies
269
views
Association study using SNP data
Association
Allele
Parentage
SNP
1 day ago by
drajangirija
• 0
2
votes
1
reply
267
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 2 days ago by
chrchang523
10k • written 6 days ago by
8armed
▴ 10
3
votes
5
replies
267
views
Generating mpileup file using samtools
mpileup
samtools
updated 3 days ago by
Joe
21k • written 3 days ago by
Ruqaiya
• 0
0
votes
4
replies
263
views
Genbank File Format
gbkformat
6 days ago by
alenew.am
• 0
1
vote
3
replies
260
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
22 hours ago by
Lada
▴ 30
0
votes
1
reply
255
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 15 hours ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
1
vote
3
replies
252
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
SJP
• 0
1
vote
2
replies
251
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
0
votes
0
replies
246
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
3 days ago by
NorbertK
• 0
0
votes
2
replies
238
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
1
vote
2
replies
235
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by
yahn
• 0
1
vote
1
reply
235
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 6 days ago by
Michael
54k • written 6 days ago by
Lissa Cruz Saavedra
• 0
1
vote
3
replies
235
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
1
vote
3
replies
234
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 3 days ago by
jared.andrews07
★ 16k • written 3 days ago by
yvonneh
▴ 10
1
vote
1
reply
232
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 5 days ago by
Ram
43k • written 5 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
228
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
1
vote
2
replies
225
views
Downloading full alignments from Pfam
pfam
1 day ago by
bef1
• 0
0
votes
1
reply
224
views
Subsetting and merging back Seurat Object brings different results
Seurat
4 days ago by
Bine
▴ 60
0
votes
1
reply
224
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 2 days ago by
Thanujay S
• 0 • written 3 days ago by
yahn
• 0
0
votes
3
replies
223
views
Question regarding WGCNA
WGCNA
Network-construction
updated 1 hour ago by
Ram
43k • written 2 days ago by
deepak
• 0
0
votes
1
reply
223
views
creating batch colum for batch correction
batch-correction
combat
6 hours ago by
Expert
▴ 10
0
votes
2
replies
221
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
37 minutes ago by
sovrappensiero
▴ 90
0
votes
1
reply
221
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 4 days ago by
Adam
▴ 30 • written 5 days ago by
J
• 0
179 results • Page
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Recent Votes
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Comment: error in R code
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Comment: Design matrix Differential expression analysis
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I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
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▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
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It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
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Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
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Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
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Got it, thank you for your response. SN
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Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
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Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
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Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
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This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
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Read the answers in the post, understand them and try to implement them.
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Just using the normalized expression of Malat1 works.
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Awesome, thank you for the concise and straight-forward answer!
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Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
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"Also if is there any other quick way to find gene specific coverage" can you give some example so that its bit more clear what do you mean…
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