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963 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
3
replies
278
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
0
replies
133
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
3 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
271
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 3 days ago by
Vijith
▴ 30
0
votes
0
replies
143
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
3 days ago by
Jeyong
• 0
0
votes
2
replies
726
views
homer not configured properly
Homer
makeTagDirectory
updated 3 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
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
0
replies
131
views
Empty table plot using plotGseaTable()
FGSEA
2 days ago by
Chris
▴ 260
0
votes
1
reply
179
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 3 days ago by
anovak
▴ 120 • written 3 days ago by
Hang
• 0
1
vote
3
replies
231
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
3
votes
5
replies
307
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
2 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 3 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
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
1
reply
210
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
updated 3 days ago by
Chris Dean
▴ 390 • written 3 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
234
views
RNA-seq data for deep learning classification
rna-seq
2 days ago by
yahn
• 0
2
votes
7
replies
421
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 3 days ago by
Qroid
▴ 40
0
votes
1
reply
509
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 3 days ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
148
views
Provean help
variant
Provean
updated 3 days ago by
Mensur Dlakic
★ 27k • written 3 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
162
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 3 days ago by
bk11
★ 2.4k • written 4 days ago by
Jeol
▴ 20
1
vote
1
reply
170
views
Super ehancers
enhancers
updated 3 days ago by
jared.andrews07
★ 16k • written 4 days ago by
Oburah
• 0
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
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
1
vote
7
replies
437
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
2 days ago by
eebloom
▴ 80
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 3 days ago by
ATpoint
82k • written 3 days ago by
alifafiq1
• 0
0
votes
0
replies
99
views
Use of annotation of integrated Seurat object in single sample
Seurat
3 days ago by
Bine
▴ 60
0
votes
0
replies
103
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 3 days ago by
Ram
43k • written 4 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
222
views
Subsetting and merging back Seurat Object brings different results
Seurat
3 days ago by
Bine
▴ 60
0
votes
0
replies
135
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 3 days ago by
Ram
43k • written 4 days ago by
4r-rtg
• 0
1
vote
1
reply
137
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 3 days ago by
Ram
43k • written 4 days ago by
marco.barr
▴ 90
0
votes
0
replies
96
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
4 days ago by
Vijith
▴ 30
9
votes
10
replies
501
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 3 days ago by
Zamin Iqbal
▴ 20 • written 4 days ago by
nicole.kavanagh
• 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
0
replies
96
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
4 days ago by
James
▴ 10
0
votes
1
reply
585
views
Basic stats in hierfstat
Fst
stats
hierfstat
updated 4 days ago by
mdav
• 0 • written 18 months ago by
Zoe
• 0
1
vote
3
replies
233
views
Odd alignment question/finding
Alignment
updated 3 days ago by
barslmn
★ 2.1k • written 4 days ago by
poordumbsillyidiot
• 0
0
votes
1
reply
206
views
GATK won't produce figures while analyzing covariates to generate 'recal_plots.pdf'
GATK
recalibration
updated 4 days ago by
GenoMax
142k • written 4 days ago by
mgranada3
▴ 30
0
votes
0
replies
98
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
4 days ago by
meck
• 0
0
votes
0
replies
124
views
Looking for the best way to interpret these data
RNA-seq
ontology
GO
updated 4 days ago by
Ram
43k • written 4 days ago by
Oscar
▴ 10
0
votes
7
replies
541
views
Post-imputation plot
michigan-imputation-server
quality-control
updated 3 days ago by
LChart
3.9k • written 6 days ago by
kl
▴ 10
0
votes
1
reply
220
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
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
0
votes
1
reply
781
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 3 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
151
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 4 days ago by
Ram
43k • written 4 days ago by
ernestine.kubi
• 0
0
votes
0
replies
106
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
4 days ago by
VITALA
• 0
1
vote
2
replies
249
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
0
votes
1
reply
183
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 4 days ago by
i.sudbery
19k • written 5 days ago by
Edmond
• 0
0
votes
0
replies
142
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
5 days ago by
O.rka
▴ 710
0
votes
1
reply
679
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 5 days ago by
Ram
43k • written 5 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
273
views
p-value in CIBERSORT
CIBERSORT
p-value
5 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
371
views
Telescope issue
Telescope
RNA-seq
updated 4 days ago by
GenoMax
142k • written 5 days ago by
eleven11
• 0
5
votes
6
replies
523
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 5 days ago by
me
▴ 760 • written 6 days ago by
Mariana
▴ 40
963 results • Page
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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
.lgen file has 3+ different alleles
Force PLINK2 to neglect chrX as the sex chromosome
Answer: Force PLINK2 to neglect chrX as the sex chromosome
LD-prune variants while maintaining a list of SNPs
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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")
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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")
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Welcome to this community. Please learn the most important lesson right away which is reading answers and learning from it. Users gave you …
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▴ 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
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snajafy
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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 …
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please could you tell me what was the solution, I am having the same problem, I only get empty files.
Comment: install package
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I also have this problem, but it doesn't work even I remove the Xms32g. The result bam is still malformed.
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This worked beautifully using 'requests.get()' in python, thank you so much!
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