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188 results • Page
2 of 4
Sort: replies
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Views
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Replies
0
votes
4
replies
260
views
Genbank File Format
gbkformat
4 days ago by
alenew.am
• 0
1
vote
4
replies
396
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
5 days ago by
hagl
▴ 10
1
vote
3
replies
242
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Qi
• 0
5
votes
3
replies
276
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 4 days ago by
Lluís R.
★ 1.2k • written 5 days ago by
이민경[학생](대학원 융합의과학과)
• 0
1
vote
3
replies
230
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 2 days ago by
Alex Reynolds
35k • written 2 days ago by
SJP
• 0
2
votes
3
replies
245
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 1 day ago by
dthorbur
★ 1.9k • written 2 days ago by
Vijith
▴ 30
1
vote
3
replies
306
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 6 days ago by
ATpoint
82k • written 7 days ago by
Francesco
▴ 10
2
votes
3
replies
235
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 6 hours ago by
Gordon Smyth
★ 7.1k • written 1 day ago by
SHN
▴ 40
1
vote
3
replies
217
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
yvonneh
▴ 10
2
votes
3
replies
728
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 15 hours ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
3
replies
284
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 4 days ago by
GenoMax
142k • written 5 days ago by
kim
• 0
1
vote
3
replies
300
views
DESeq2 processing problems
deseq2
R
updated 3 days ago by
ATpoint
82k • written 3 days ago by
jagdish7921
• 0
1
vote
3
replies
278
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 4 days ago by
GenoMax
142k • written 4 days ago by
jeffrey.maurer.informatics
• 0
0
votes
3
replies
401
views
why renaming Idents in Seurat object doesn't work?
Seurat
RenameIdents
R
4 days ago by
Assa Yeroslaviz
★ 1.8k
1
vote
3
replies
394
views
PCA plot
DESeq2
PCAplot
updated 6 days ago by
LauferVA
4.2k • written 10 days ago by
Aaliya
▴ 10
3
votes
3
replies
323
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 5 days ago by
noodle
▴ 580 • written 6 days ago by
WUSCHEL
▴ 750
1
vote
3
replies
222
views
Odd alignment question/finding
Alignment
updated 1 day ago by
barslmn
★ 2.1k • written 3 days ago by
poordumbsillyidiot
• 0
0
votes
3
replies
216
views
Software to separate reads from different individuals
software
development
nanopore
updated 5 days ago by
GenoMax
142k • written 5 days ago by
njornet
▴ 20
3
votes
3
replies
300
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 1 day ago by
ATpoint
82k • written 2 days ago by
alifafiq1
• 0
1
vote
3
replies
396
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 6 days ago by
Mensur Dlakic
★ 27k • written 8 days ago by
O.rka
▴ 710
0
votes
3
replies
337
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 5 days ago by
Ram
43k • written 4 months ago by
Fadi
• 0
0
votes
3
replies
743
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 5 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
3
replies
279
views
KEGG Pathways
r
RNA-seq
updated 4 days ago by
Ram
43k • written 4 days ago by
Sudip
• 0
1
vote
2
replies
226
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
2
votes
2
replies
205
views
PDB related issue
rcsb
pdb
updated 6 days ago by
noodle
▴ 580 • written 6 days ago by
Nafi
• 0
3
votes
2
replies
299
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 5 days ago by
i.sudbery
19k • written 8 days ago by
vanbelj
▴ 40
0
votes
2
replies
160
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
5 days ago by
Lluís R.
★ 1.2k
0
votes
2
replies
226
views
How to update R on ubuntu
installation
update
R
apt-get
5 days ago by
Bosberg
▴ 50
4
votes
2
replies
305
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
0
votes
2
replies
205
views
What should I consider as FASTA for dataset?
PDB
FASTA
5 days ago by
Nafi
• 0
2
votes
2
replies
198
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 5 days ago by
ATpoint
82k • written 5 days ago by
Sudip
• 0
0
votes
2
replies
227
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 4 days ago by
GenoMax
142k • written 4 days ago by
Dora
▴ 10
1
vote
2
replies
225
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 4 days ago by
Ram
43k • written 5 days ago by
Ravita
• 0
3
votes
2
replies
378
views
Extract protein sequence
fasta
alignment
blast
4 days ago by
anna
▴ 20
2
votes
2
replies
266
views
p-value in CIBERSORT
CIBERSORT
p-value
3 days ago by
michelafrancesconi9
▴ 20
1
vote
2
replies
285
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
3 days ago by
Nafi
• 0
1
vote
2
replies
245
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
3 days ago by
rianna.collins
• 0
0
votes
2
replies
180
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
2 days ago by
dtnondorf
• 0
0
votes
2
replies
707
views
homer not configured properly
Homer
makeTagDirectory
updated 2 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
2
replies
277
views
read length in structural variant calling
nanopore
SV
QC
ONT
variant
1 day ago by
eebloom
▴ 80
0
votes
2
replies
154
views
Raw counts using stringtie
stringtie
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 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 1 day ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
0
votes
2
replies
190
views
Downloading older version of a tool
Alignment
tools
1 day ago by
Ruqaiya
• 0
2
votes
2
replies
2.6k
views
Pindel Segmentation Fault Error
pindel
updated 19 hours ago by
Ruqaiya
• 0 • written 10.2 years ago by
Yuelin
▴ 20
0
votes
2
replies
147
views
creating batch colum for batch correction
batch-correction
combat
updated 12 hours ago by
Ram
43k • written 20 hours ago by
Expert
▴ 10
2
votes
2
replies
176
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 12 hours ago by
Ram
43k • written 1 day ago by
carolofharvest
▴ 30
4
votes
2
replies
133
views
GRCh38.gmap file
gnomix
gmap
9 hours ago by
lorena9132
▴ 10
1
vote
2
replies
1.0k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
30 minutes ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
143
views
Provean help
variant
Provean
updated 2 days ago by
Mensur Dlakic
★ 27k • written 2 days ago by
Arun Sai Kumar
• 0
0
votes
1
reply
271
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 3 days ago by
Scooter
▴ 280 • written 9 days ago by
avocado123
• 0
188 results • Page
2 of 4
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Recent Replies
Comment: The GDC Legacy Archive is retiring soon.
by
Zhenyu Zhang
★ 1.2k
If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Zhenyu Zhang
★ 1.2k
These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
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