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682 results • Page
7 of 14
Sort: Rank
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Votes
Replies
0
votes
1
reply
236
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 14 days ago by
Ram
43k • written 15 days ago by
Rob
▴ 170
0
votes
2
replies
279
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 8 days ago by
GenoMax
142k • written 15 days ago by
Ximena
• 0
0
votes
1
reply
222
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 15 days ago by
Ram
43k • written 15 days ago by
Valentina
• 0
0
votes
6
replies
491
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 15 days ago by
swbarnes2
14k • written 15 days ago by
Erina
• 0
1
vote
3
replies
343
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
13 days ago by
Lada
▴ 30
1
vote
0
replies
161
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 13 days ago by
zx8754
11k • written 15 days ago by
Emilie
▴ 10
0
votes
0
replies
148
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
15 days ago by
Javier
• 0
0
votes
2
replies
310
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 15 days ago by
yahn
• 0
0
votes
0
replies
140
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
15 days ago by
mikemakaveli1
• 0
2
votes
2
replies
253
views
Raw counts using stringtie
stringtie
RNA-seq
updated 15 days ago by
GenoMax
142k • written 15 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
139
views
Modify plot R mtDNA indel
plot
mtDNA
R
15 days ago by
marco.barr
▴ 130
0
votes
0
replies
339
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
15 days ago by
NorbertK
▴ 10
4
votes
2
replies
271
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 14 days ago by
Ram
43k • written 16 days ago by
carolofharvest
▴ 40
13
votes
14
replies
963
views
High Malat-1 expression in single cell data
single-cell
updated 11 days ago by
t.montserrat.ayuso
▴ 40 • written 20 days ago by
carolofharvest
▴ 40
0
votes
2
replies
289
views
Downloading older version of a tool
Alignment
tools
15 days ago by
Ruqaiya
• 0
0
votes
0
replies
162
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
16 days ago by
rustykb
▴ 20
1
vote
1
reply
207
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 14 days ago by
Ram
43k • written 16 days ago by
adi.gershon1
• 0
3
votes
5
replies
350
views
Generating mpileup file using samtools
mpileup
samtools
updated 16 days ago by
Joe
21k • written 16 days ago by
Ruqaiya
• 0
0
votes
5
replies
446
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 16 days ago by
b.contreras.moreira
▴ 200 • written 16 days ago by
JH
• 0
1
vote
3
replies
323
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 16 days ago by
ATpoint
82k • written 16 days ago by
Qi
• 0
0
votes
0
replies
149
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
16 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
333
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 15 days ago by
dthorbur
★ 2.0k • written 16 days ago by
Vijith
▴ 30
0
votes
0
replies
163
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
16 days ago by
Jeyong
• 0
0
votes
2
replies
756
views
homer not configured properly
Homer
makeTagDirectory
updated 16 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
3
replies
328
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 16 days ago by
Alex Reynolds
35k • written 16 days ago by
SJP
• 0
0
votes
0
replies
153
views
Empty table plot using plotGseaTable()
FGSEA
15 days ago by
Chris
▴ 280
0
votes
1
reply
220
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 16 days ago by
anovak
▴ 120 • written 16 days ago by
Hang
• 0
1
vote
3
replies
292
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 16 days ago by
jared.andrews07
★ 16k • written 16 days ago by
yvonneh
▴ 10
3
votes
5
replies
411
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
15 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 16 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
245
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
16 days ago by
dtnondorf
• 0
3
votes
8
replies
712
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 12 days ago by
Chris Dean
▴ 410 • written 16 days ago by
sovrappensiero
▴ 100
1
vote
2
replies
284
views
RNA-seq data for deep learning classification
rna-seq
16 days ago by
yahn
• 0
3
votes
8
replies
632
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
12 days ago by
Qroid
▴ 40
0
votes
1
reply
551
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 16 days ago by
Hugo
• 0 • written 5 months ago by
Rachel
• 0
0
votes
1
reply
185
views
Provean help
variant
Provean
updated 16 days ago by
Mensur Dlakic
★ 27k • written 16 days ago by
Arun Sai Kumar
• 0
1
vote
1
reply
195
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 16 days ago by
bk11
★ 2.5k • written 17 days ago by
Jeol
▴ 20
1
vote
1
reply
202
views
Super ehancers
enhancers
updated 16 days ago by
jared.andrews07
★ 16k • written 17 days ago by
Oburah
• 0
4
votes
7
replies
431
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
5 days ago by
Chen
• 0
5
votes
5
replies
357
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 16 days ago by
atharvakarkare14
▴ 40 • written 17 days ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
512
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
16 days ago by
eebloom
▴ 80
3
votes
3
replies
384
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 16 days ago by
ATpoint
82k • written 17 days ago by
alifafiq1
• 0
0
votes
0
replies
115
views
Use of annotation of integrated Seurat object in single sample
Seurat
17 days ago by
Bine
▴ 60
0
votes
0
replies
124
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 16 days ago by
Ram
43k • written 17 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
265
views
Subsetting and merging back Seurat Object brings different results
Seurat
16 days ago by
Bine
▴ 60
0
votes
0
replies
188
views
Job:
Postdoctoral Position in Bioinformatics - Mainz, Germany
NGS
Genomics
Post-doc
R-loops
updated 16 days ago by
Ram
43k • written 17 days ago by
4r-rtg
• 0
1
vote
1
reply
170
views
Discrepancy in read counts from fastq
downsampling
fastq
updated 16 days ago by
Ram
43k • written 17 days ago by
marco.barr
▴ 130
0
votes
0
replies
111
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
17 days ago by
Vijith
▴ 30
10
votes
14
replies
800
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
updated 11 days ago by
GenoMax
142k • written 17 days ago by
nicole.kavanagh
• 0
0
votes
1
reply
300
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
updated 17 days ago by
Scooter
▴ 280 • written 23 days ago by
avocado123
• 0
682 results • Page
7 of 14
Recent Votes
plotting trees in R: node labels from nexus tree files
Interpreting the Jackstraw plot of Seurat
A: How is the design in DESeq2 work?
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
Answer: RNAseq coverage vs depth for transcript isoform expression?
constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
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Popular Question
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carlopecoraro2
★ 2.5k
Popular Question
to
scideas
▴ 30
Popular Question
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Muhammad
• 0
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synat.keam
▴ 100
Scholar
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jv
★ 1.8k
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Recent Replies
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from
by
ATpoint
82k
Use everything before the whitespace in list.txt, for example `A00869:294:HCW57DSXY:2:1101:3929:1000` and not `A00869:294:HCW57DSXY:2:1101:…
Answer: CellRanger output more cells than specified using --force-cells? Why?
by
scideas
▴ 30
I actually had this same issue with CellRanger v7- turns out that since you have 2 species in your mapping reference, CellRanger is forcing…
Answer: Checking chromosome builds for genotyping data
by
Muhammad
• 0
Assume you have genotype data in Plink format. (G.bed, G.bim, G.fam) Download some reference panel data in Plink format (R.bed, R.bim, R.f…
Comment: Error in CIBERSORTx ($ operator is invalid for atomic vectors)
by
nguyenn6
• 0
did you ever figure it out? i'm having the same issue.
Comment: Traveler with Infernal mapping failed
by
anton.i.petrov
• 0
Hi Larissa! I am the lead developer of R2DT and I've just noticed this question. Could you please email help@r2dt.bio with your input seque…
Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform estimation precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167.…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
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