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189 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
0
votes
3
replies
340
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 6 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
1
vote
6
replies
338
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 2 days ago by
GenoMax
142k • written 20 days ago by
eebloom
▴ 80
0
votes
5
replies
334
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 2 days ago by
b.contreras.moreira
▴ 180 • written 3 days ago by
JH
• 0
1
vote
5
replies
328
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
2 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
3
votes
3
replies
310
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 2 days ago by
ATpoint
82k • written 3 days ago by
alifafiq1
• 0
2
votes
3
replies
309
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 1 day ago by
Gordon Smyth
★ 7.1k • written 2 days ago by
SHN
▴ 40
0
votes
5
replies
307
views
RNAseq one control two conditions, shared and exclusive genes
conditions
RNAseq
multiple
Rstudio
updated 2 days ago by
Mohamed Abderrahmane
▴ 20 • written 6 days ago by
matteo.levorato
• 0
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
306
views
DESeq2 processing problems
deseq2
R
updated 4 days ago by
ATpoint
82k • written 4 days ago by
jagdish7921
• 0
3
votes
5
replies
305
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
2 days ago by
Maverick
▴ 10
0
votes
5
replies
301
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 2 days ago by
chrchang523
10k • written 2 days ago by
curious
▴ 750
3
votes
2
replies
299
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 days ago by
i.sudbery
19k • written 9 days ago by
vanbelj
▴ 40
0
votes
3
replies
293
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 5 days ago by
GenoMax
142k • written 6 days ago by
kim
• 0
2
votes
4
replies
292
views
from row count to tpm
tpm
row-count
normalization
updated 5 days ago by
Ram
43k • written 13 days ago by
michelafrancesconi9
▴ 20
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
4 days ago by
Nafi
• 0
0
votes
1
reply
287
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
5 days ago by
David Langenberger
11k
0
votes
6
replies
286
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 2 days ago by
dsull
★ 6.0k • written 3 days ago by
Chen
• 0
1
vote
4
replies
285
views
Segmentation error while using a tool
smalt
updated 1 day ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Ruqaiya
• 0
0
votes
3
replies
283
views
KEGG Pathways
r
RNA-seq
updated 5 days ago by
Ram
43k • written 5 days ago by
Sudip
• 0
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 5 days ago by
Lluís R.
★ 1.2k • written 6 days ago by
이민경[학생](대학원 융합의과학과)
• 0
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 5 days ago by
jeffrey.maurer.informatics
• 0
1
vote
2
replies
278
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
2 days ago by
eebloom
▴ 80
0
votes
1
reply
277
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 17 hours ago by
GenoMax
142k • written 1 day ago by
tulip
• 0
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
0
votes
1
reply
274
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 6 days ago by
trausch
★ 1.9k • written 23 days ago by
zec018
• 0
1
vote
3
replies
274
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Qi
• 0
2
votes
2
replies
273
views
p-value in CIBERSORT
CIBERSORT
p-value
4 days ago by
michelafrancesconi9
▴ 20
0
votes
4
replies
273
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
2
votes
3
replies
270
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 2 days ago by
dthorbur
★ 1.9k • written 2 days ago by
Vijith
▴ 30
5
votes
5
replies
268
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 3 days ago by
atharvakarkare14
▴ 30 • written 3 days ago by
Begonia_pavonina
▴ 150
0
votes
4
replies
262
views
Genbank File Format
gbkformat
5 days ago by
alenew.am
• 0
3
votes
5
replies
257
views
Generating mpileup file using samtools
mpileup
samtools
updated 2 days ago by
Joe
21k • written 2 days ago by
Ruqaiya
• 0
1
vote
3
replies
250
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
SJP
• 0
0
votes
1
reply
249
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 2 days ago by
chrchang523
10k • written 5 days ago by
8armed
• 0
1
vote
2
replies
246
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
1
vote
3
replies
244
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
1 hour ago by
Dora
▴ 10
1
vote
2
replies
234
views
RNA-seq data for deep learning classification
rna-seq
2 days ago by
yahn
• 0
1
vote
1
reply
233
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 5 days ago by
Michael
54k • written 6 days ago by
Lissa Cruz Saavedra
• 0
1
vote
3
replies
232
views
Odd alignment question/finding
Alignment
updated 2 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
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
231
views
Association study using SNP data
Association
Allele
Parentage
SNP
15 hours ago by
drajangirija
• 0
0
votes
2
replies
230
views
How to update R on ubuntu
installation
update
R
apt-get
6 days ago by
Bosberg
▴ 50
1
vote
3
replies
230
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
12 hours ago by
Lada
▴ 30
1
vote
3
replies
229
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
0
votes
1
reply
229
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 5 hours ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
0
votes
0
replies
229
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
6 days ago by
SSSJec
• 0
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 5 days ago by
Ram
43k • written 5 days ago by
Ravita
• 0
0
votes
0
replies
228
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
2 days ago by
NorbertK
• 0
0
votes
2
replies
225
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
189 results • Page
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Recent Votes
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Answer: Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so t
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swbarnes2
14k
Any chance the numerical columns were imported as factors?
Comment: ERROR When Using Ensembl Plants Biomart Wget API
by
Dora
▴ 10
Thank you very much, that works perfectly :) ! Maybe someone needs to use a plant dataset as an example (instead of human dataset ) in the …
Comment: Truncated Bam Error
by
guanghao
• 0
I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
Answer: DMRcate ranges liftover hg19 to hg38
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Hey, I believe they are mapped to hg19 and this is potentially a bigger problem than people realise, I nearly made this mistake and I would…
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This worked beautifully using 'requests.get()' in python, thank you so much!
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first get the main ID in stringdb: $ wget -qO - "https://string-db.org/api/tsv-no-header/get_string_ids?identifiers=RPS4Y1&species=960…
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if I understood correctly, I might need fle `prot.accession2taxid.gz` file? According to the [documentation][1] in column 2 is Accession.ve…
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To follow on Mathew's reply, one way might be to try and see if you can download and install the package tarball locally: 1. Get the packag…
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God bless you man.
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thank you, I'll look at these files/documents. .
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Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
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