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183 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
1
vote
3
replies
272
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
8 hours ago by
Dora
▴ 10
3
votes
3
replies
311
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
1
vote
3
replies
254
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
19 hours ago by
Lada
▴ 30
1
vote
3
replies
232
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
3
replies
279
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
0
votes
3
replies
413
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
5 days ago by
Assa Yeroslaviz
★ 1.8k
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
0
votes
3
replies
220
views
Software to separate reads from different individuals
software
development
nanopore
updated 6 days ago by
GenoMax
142k • written 6 days ago by
njornet
▴ 20
1
vote
3
replies
251
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 3 days ago by
Alex Reynolds
35k • written 3 days ago by
SJP
• 0
0
votes
3
replies
744
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 6 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
3
replies
293
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 6 days ago by
GenoMax
142k • written 6 days ago by
kim
• 0
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
2
votes
3
replies
778
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 1 day ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
1
vote
3
replies
234
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 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
1
vote
3
replies
306
views
DESeq2 processing problems
deseq2
R
updated 4 days ago by
ATpoint
82k • written 5 days ago by
jagdish7921
• 0
2
votes
3
replies
320
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
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
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
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
2
votes
2
replies
206
views
Raw counts using stringtie
stringtie
RNA-seq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
ahmad.sajad4541
• 0
2
votes
2
replies
201
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Sudip
• 0
0
votes
2
replies
232
views
How to update R on ubuntu
installation
update
R
apt-get
6 days ago by
Bosberg
▴ 50
0
votes
2
replies
134
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 10 minutes ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
1
vote
2
replies
280
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
3 days ago by
eebloom
▴ 80
2
votes
2
replies
168
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
14 hours ago by
brandon
• 0
2
votes
2
replies
257
views
Association study using SNP data
Association
Allele
Parentage
SNP
22 hours ago by
drajangirija
• 0
1
vote
2
replies
224
views
Downloading full alignments from Pfam
pfam
23 hours ago by
bef1
• 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 6 days ago by
Ravita
• 0
3
votes
2
replies
383
views
Extract protein sequence
fasta
alignment
blast
5 days ago by
anna
▴ 20
0
votes
2
replies
144
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 40 minutes ago by
GenoMax
142k • written 17 hours ago by
mropri
▴ 150
1
vote
2
replies
1.1k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
1 day ago by
Zhenyu Zhang
★ 1.2k
2
votes
2
replies
274
views
p-value in CIBERSORT
CIBERSORT
p-value
5 days ago by
michelafrancesconi9
▴ 20
1
vote
2
replies
234
views
RNA-seq data for deep learning classification
rna-seq
3 days ago by
yahn
• 0
4
votes
2
replies
204
views
GRCh38.gmap file
gnomix
gmap
1 day ago by
lorena9132
▴ 10
2
votes
2
replies
214
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 1 day ago by
Ram
43k • written 3 days ago by
carolofharvest
▴ 30
1
vote
2
replies
250
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 2 days ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
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
0
votes
2
replies
235
views
Downloading older version of a tool
Alignment
tools
2 days ago by
Ruqaiya
• 0
0
votes
2
replies
206
views
What should I consider as FASTA for dataset?
PDB
FASTA
6 days ago by
Nafi
• 0
0
votes
2
replies
189
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
3 days ago by
dtnondorf
• 0
0
votes
2
replies
727
views
homer not configured properly
Homer
makeTagDirectory
updated 3 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
2
votes
2
replies
1.8k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 2 days ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
0
votes
1
reply
174
views
unable to get feature count results
featureCounts
updated 5 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
0
votes
1
reply
169
views
metagenomic virome quality assessment
viromics
metagenomics
updated 6 days ago by
Ram
43k • written 6 days ago by
Petchimuthu
• 0
0
votes
1
reply
183
views
Differential Accessibility
DiffBind
updated 6 days ago by
Ram
43k • written 6 days ago by
Shloka
• 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
0
votes
1
reply
189
views
Deseq2
Deseq2
updated 6 days ago by
Jack Tierney
▴ 360 • written 6 days ago by
Sudip
• 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
183 results • Page
2 of 4
Recent Votes
UMI-Tools 0.5, now with tools for cell barcoded scRNA-seq
Comment: install.packages("imudata")
Answer: Can I merge Hi-C fastq files from different lanes?
Answer: Interpretation of output from MiXCR TCR sequencing
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
Answer: Association study using SNP data
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Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
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…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
Comment: Gene Specific coverage from WGS data
by
1769mkc
★ 1.2k
"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…
Answer: Tissue-specific DEG analysis with DEseq2
by
ATpoint
82k
I assume that all data are from the same experiment, without batch effects and can thus be quantitiatively compared: Many ways to do thi…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
snajafy
• 0
I am facing the same problem and I don't know how to solve the problem,....
Comment: install.packages("imudata")
by
zx8754
11k
[How should I deal with "package 'xxx' is not available (for R version x.y.z)" warning?](https://stackoverflow.com/q/25721884/680068)
Answer: install.packages("imudata")
by
ATpoint
82k
Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
Comment: install.packages("imudata")
by
marco.barr
▴ 90
You can install from github directly. Many R packages are not present in the CRAN repository or in Bioconductor( from Biocmanager). Also re…
Comment: install package
by
snajafy
• 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' removing 'C:/Users/najafi/AppData/…
Comment: Quetion regarding WGCNA
by
andres.firrincieli
3.6k
There is something wrong with your data but without any context I can't really answer to your question. I would like to see a PCA plot of …
Comment: error to run rnammer
by
antonio.spl
• 0
please could you tell me what was the solution, I am having the same problem, I only get empty files.
Comment: install package
by
snajafy
• 0
Hi, Thanks for your answer, I do it, but I get this error: ERROR: compilation failed for package 'gmwm' * removing 'C:/Users/najafi/AppData…
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