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306 results • Page
3 of 7
Sort: Views
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Views
Votes
Replies
1
vote
3
replies
298
views
Requesting further clarification on interpreting relative gene expression strength
R
normalization
TPM
RNA-seq
DESeq2
updated 12 days ago by
ATpoint
76k • written 26 days ago by
Abhishek
• 0
0
votes
4
replies
293
views
Split reads along the genome in my samples
DNA
sequencing
12 days ago by
paulaotero.sanchez
• 0
0
votes
2
replies
292
views
ClusterProfiler GeneRatio demoninator not the same for all values
enrichment-analysis
clusterprofiler
RNA-seq
deseq2
19 days ago by
Lily
• 0
0
votes
2
replies
291
views
Deseq2 colData for single condition
RNA-seq
9 days ago by
Petesview
• 0
1
vote
4
replies
290
views
rRNA filtering from human RNA-seq data
rRNA
RNA-seq
6 days ago by
deniz
▴ 10
2
votes
3
replies
287
views
Genewise output help
genewise
updated 7 days ago by
Jean-Karim Heriche
26k • written 7 days ago by
lorenzoedg
• 0
1
vote
2
replies
286
views
Adjusting covariate in regression model
regression
statistics
25 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
283
views
functional analysis prediction
functionalanalysis
metabarcoding
16S
8 days ago by
safeassli
• 0
5
votes
3
replies
281
views
Visualisation of accessible regions in single cell atacseq data
visualization
scATAC-seq
single-cell
updated 11 days ago by
Ram
40k • written 11 days ago by
sarahmanderni
▴ 90
0
votes
2
replies
279
views
miRNAseq - over-presented sequence in negative control
miRNAseq
adaptor
dimer
14 days ago by
MH85
• 0
2
votes
3
replies
278
views
Can I infer the fraction of replicating cells from bulk RNA-seq data?
replication
apoptosis
updated 5 days ago by
Ram
40k • written 5 days ago by
txema.heredia
▴ 80
1
vote
3
replies
275
views
Question regarding MACS2 approach of peak calling
MACS2
sequencing-depth
chipseq
updated 6 days ago by
ATpoint
76k • written 14 days ago by
rkc5
• 0
0
votes
3
replies
275
views
Extracting/assembling organellar reads from RNAseq data
transcriptome
star
alignment
mapping
updated 7 days ago by
LChart
3.3k • written 14 days ago by
Miles
• 0
0
votes
1
reply
275
views
computeMatrix error: [pyBwOpen] bw is NULL!
deeptools
bigWig
computeMatrix
updated 22 days ago by
rfran010
▴ 790 • written 24 days ago by
bp22
▴ 30
0
votes
2
replies
273
views
Gene Ontology - How to do Transcript Ontology?
gene-ontology
GO
transcripts
updated 14 days ago by
Ram
40k • written 16 days ago by
Lakritz the LabRat
• 0
0
votes
0
replies
272
views
GTF/Reference genome adjustments? Gene-based differential expression analysis of genetically modified mouse line
RNA-seq
DGE
updated 7 days ago by
Ram
40k • written 8 days ago by
alex
• 0
1
vote
2
replies
272
views
Dotplot error: subscript out of bound
R
scRNA-seq
seurat
2 days ago by
Xuhao
• 0
0
votes
4
replies
270
views
Analyzing time-patterns in RNA Seq data only having results_apeglm
R
sequencing
12 days ago by
Paul
• 0
1
vote
2
replies
270
views
Multiple testing adjustment for stepwise model selection
statistics
8 days ago by
mel22
▴ 100
1
vote
5
replies
267
views
Calculation of TMB on gene level
genomics
updated 2 hours ago by
Zhenyu Zhang
▴ 980 • written 22 hours ago by
smrutimayipanda
▴ 20
2
votes
4
replies
268
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
2 days ago by
Grace
• 0
0
votes
3
replies
267
views
Genomic location of MUC16
VNTR
genome
updated 18 days ago by
GenoMax
134k • written 21 days ago by
fi1d18
★ 4.2k
1
vote
1
reply
267
views
Which reference genome, DNA or cDNA and why?
or
DNA
cDNA
updated 22 days ago by
GenoMax
134k • written 23 days ago by
وفاء
• 0
1
vote
4
replies
267
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
1 day ago by
Athena
• 0
0
votes
2
replies
267
views
STAR mapping two pass mode for multiple samples with split steps or one step ?
STAR
RNA-seq
14 days ago by
octpus616
▴ 80
0
votes
1
reply
265
views
WGCNA
WGCNA
Degree
igraph
updated 23 days ago by
LauferVA
3.7k • written 23 days ago by
Mehwish
• 0
0
votes
3
replies
265
views
How to find target genes From RNA seq data?
Cotton
DGE
RNA-seq
updated 6 days ago by
Ram
40k • written 6 days ago by
Fizzah
▴ 30
2
votes
2
replies
265
views
Pangenome using Orthofinder
OrthoFinder
Pangenome
bacteria
8 days ago by
kirankumareripogu
▴ 10
0
votes
2
replies
264
views
Poly-A trimming for WGBS
Trimgalore
FastP
Poly-A
26 days ago by
Keem Uarren Eiryll
• 0
0
votes
2
replies
264
views
Is there a way to visualize RNA fold in R
fold
secondary
R
structure
RNA
updated 26 days ago by
biofalconch
▴ 980 • written 27 days ago by
Serij´s
• 0
0
votes
2
replies
263
views
circRNA isolation
circular-RNA
circRNA
cDNA
11 days ago by
dbagmerve
• 0
0
votes
2
replies
262
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
2 days ago by
Mo
▴ 40
0
votes
2
replies
260
views
Extract reference and alternate SNPs for different samples
vcftools
bcftools
SNPs
updated 18 days ago by
GenoMax
134k • written 18 days ago by
gubrins
▴ 270
0
votes
2
replies
255
views
Change mounted drive on GCP Batch nextflow process
google-cloud-platform
unix
nextflow
29 days ago by
dthorbur
▴ 550
5
votes
4
replies
251
views
Low Alignment rate
alignment
low_alignment_rate
Bowtie2
14 hours ago by
Mehwish
• 0
0
votes
3
replies
252
views
Errors while trying to run Scenic
Scenic
updated 6 days ago by
GenoMax
134k • written 6 days ago by
Stavroula
• 0
0
votes
2
replies
250
views
Assigning GO ids to blast hits
Linux
GO
blast
18 days ago by
Mousumi Akter
• 0
0
votes
0
replies
247
views
getSex warning in minfi - what is the distinction between the two sex prediction methods?
methylation
ewas
minfi
24 days ago by
rkb965
• 0
1
vote
1
reply
246
views
Bioconductor Package Installation
bioconductor
updated 11 days ago by
Ram
40k • written 11 days ago by
oduduabasi.isaiah
• 0
0
votes
3
replies
246
views
CNV using GISTIC
CNV
GISTIC
updated 12 days ago by
Ram
40k • written 12 days ago by
ananta.kapoor
• 0
0
votes
2
replies
245
views
Volunteer projects in 2023 for new bioinformaticians
junior
volunteer
projects
18 days ago by
gallardodiazmiriam
▴ 20
0
votes
2
replies
243
views
Picking parameters for QC of long-read data?
long-read
nanopore
qc
qualiy-control
19 days ago by
Gio
• 0
0
votes
1
reply
242
views
How to predict/annotate whether some type strains has a certain type of enzyme?
genome
gene
blast
annotation
updated 17 days ago by
GenoMax
134k • written 17 days ago by
JyiYeung
• 0
1
vote
1
reply
239
views
Some problem about heatmap of scRNA-seq
scRNA-seq
heatmap
updated 18 days ago by
LauferVA
3.7k • written 18 days ago by
feather-W
• 0
1
vote
1
reply
239
views
GISTIC CNV
Gistic
updated 17 days ago by
Ram
40k • written 17 days ago by
ananta.kapoor
• 0
0
votes
1
reply
239
views
Filtered methylated sites annotation
methylation
annotation
TCGA
updated 24 days ago by
Ram
40k • written 24 days ago by
dilrajkaur766
• 0
0
votes
0
replies
238
views
About finding the best transcript form the target to query
blast
updated 27 days ago by
Ram
40k • written 7 weeks ago by
sk2783
• 0
1
vote
3
replies
238
views
Sub-sampleing bam files based on sequencing_summary.txt (guppy output)
samtools
guppy
updated 5 days ago by
GenoMax
134k • written 5 days ago by
anika.john
• 0
0
votes
2
replies
237
views
Segmentation fault error in CONTROL-FREEC
copy-number-variants
FREEC
14 days ago by
DdogBoss
• 0
1
vote
1
reply
235
views
ERROR Running EDTA
Transposon
updated 24 days ago by
Ram
40k • written 24 days ago by
manaswiniparija3
▴ 10
306 results • Page
3 of 7
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geom_signif() uses t-test to compare between more than 3 groups... Isn't this wrong?
Answer: Filter transcription factors
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Recent Replies
Comment: gene correlations in between two groups
by
ATpoint
76k
And how should I know this? I cannot read minds, nor see your screen, data or anything. Please ask a good question with necessary details. …
Comment: gene correlations in between two groups
by
edus_bioinfo
▴ 40
Thanks. But they are already analyzed. Afaik it analyzes raw data. In my dataset for each gene there is score. I want to interpret the data…
Answer: GWAS phenotype
by
dthorbur
▴ 550
Hello again. Yes, you can conduct GWAS using binary trait data, but it comes with a whole suite of complications. See [this](https://ww…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
RM123
▴ 10
Hello Dariober, That seems like a good solution, however I'm pretty new to R. Could you tell me how I can do that?
Comment: how to create a loop in R
by
Nicolas Rosewick
10k
Not really a bioinformatics related question. Start by looking at R tutorial, there is plenty of them online e.g. : https://www.statmethods…
Comment: Violin plot (Monocle 3) - Troubleshooting
by
fracarb8
★ 1.2k
You did not add the screenshot.
Answer: BED files
by
Alex Reynolds
35k
Generically via `bedmap`: ``` bedmap --echo --echo-map --count exome.bed annotations.bed > answer.bed ``` The `annotations.bed` fil…
Comment: geom_signif() uses t-test to compare between more than 3 groups... Isn't this wr
by
dariober
14k
It seems to me that anova followed by HSD is a more sensible approach than applying independent t-tests. Granted this is the first time I s…
Comment: BED files
by
barslmn
★ 1.8k
I am guessing you want the annotation files. https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/
Comment: Filter human transcription factors
by
Alex Reynolds
35k
Curious how redundant these TFs are. Jeff Vierstra has done some analysis on this to simplify model sets: https://www.vierstra.org/resource…
Comment: Read block operation failed with BAM file
by
Alex Reynolds
35k
https://github.com/samtools/htslib/pull/1676 patches a seek issue in `htslib` (upon which `samtools` and `pysam` depend)
Comment: Merging the filename with tsv files for master file
by
barslmn
★ 1.8k
Could you add samples from your files and your expected output.
Comment: Download an example of fully-imputed VCF files ?
by
barslmn
★ 1.8k
Check out the 1000 genomes project. https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/
Comment: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★ 1.2k
Sorry my mistake! it’s been a minute since I’ve used these sites. Yes that it is common place, what is the goal of your analysis using th…
Comment: gene correlations in between two groups
by
ATpoint
76k
Use specialized software to analyse CRISPR/RNAi data, such as MAGeCK.
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