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116,750 results • Page
1 of 2335
Sort: Rank
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0
votes
0
replies
12
views
Quetion regarding WGCNA
WGCNA
Network
construction
44 minutes ago by
deepak180001
• 0
0
votes
0
replies
14
views
Design matrix Differential expression analysis
expression
designmatrix
analysis
Differential
RNA-sequence
1 hour ago by
SHN
▴ 40
0
votes
1
reply
46
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 1 hour ago by
bk11
★ 2.4k • written 2 hours ago by
Rob
▴ 170
0
votes
0
replies
33
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
2 hours ago by
Ximena
• 0
0
votes
0
replies
28
views
filtering before dada2
metagenomic
bbduk
qiime2
dada2
bioinformatics
2 hours ago by
Valentina
• 0
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
6
replies
218
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 2 hours ago by
swbarnes2
14k • written 9 hours ago by
Erina
• 0
0
votes
1
reply
55
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 3 hours ago by
swbarnes2
14k • written 3 hours ago by
kalavattam
▴ 190
0
votes
1
reply
58
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 4 hours ago by
GenoMax
142k • written 4 hours ago by
Lada
▴ 30
0
votes
0
replies
45
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
6 hours ago by
Emilie
• 0
0
votes
4
replies
136
views
Easy way to find out which allele is minor allele from bed file?
plink
4 hours ago by
curious
▴ 750
0
votes
0
replies
38
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
6 hours ago by
Javier
• 0
0
votes
0
replies
37
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
7 hours ago by
yahn
• 0
0
votes
0
replies
45
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
7 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
45
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 7 hours ago by
Ram
43k • written 7 hours ago by
M.
▴ 30
0
votes
2
replies
98
views
Raw counts using stringtie
stringtie
RNA-seq
updated 7 hours ago by
GenoMax
142k • written 8 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
42
views
Modify plot R mtDNA indel
plot
mtDNA
R
9 hours ago by
marco.barr
▴ 90
0
votes
0
replies
46
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
9 hours ago by
NorbertK
• 0
2
votes
2
replies
122
views
Analysis of intronic reads included scRNA-seq data
cell
single
updated 9 hours ago by
t.montserrat.ayuso
▴ 10 • written 13 hours ago by
carolofharvest
▴ 30
9
votes
9
replies
443
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 7 hours ago by
dsull
★ 6.0k • written 4 days ago by
carolofharvest
▴ 30
0
votes
1
reply
87
views
Downloading older version of a tool
Alignment
tools
updated 10 hours ago by
GenoMax
142k • written 11 hours ago by
Ruqaiya
• 0
0
votes
0
replies
58
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
11 hours ago by
rustykb
▴ 20
1
vote
1
reply
80
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 13 hours ago by
ATpoint
82k • written 13 hours ago by
adi.gershon1
• 0
3
votes
5
replies
174
views
Generating mpileup file using samtools
mpileup
samtools
updated 10 hours ago by
Joe
21k • written 13 hours ago by
Ruqaiya
• 0
0
votes
5
replies
238
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 14 hours ago by
b.contreras.moreira
▴ 180 • written 1 day ago by
JH
• 0
1
vote
3
replies
194
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 15 hours ago by
ATpoint
82k • written 1 day ago by
Qi
• 0
0
votes
0
replies
58
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
16 hours ago by
Amos Bairoch
▴ 120
1
vote
3
replies
168
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 7 hours ago by
dthorbur
★ 1.9k • written 16 hours ago by
Vijith
▴ 30
0
votes
0
replies
78
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
17 hours ago by
Jeyong
• 0
0
votes
2
replies
665
views
homer not configured properly
Homer
makeTagDirectory
updated 19 hours ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
178
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 20 hours ago by
Alex Reynolds
35k • written 1 day ago by
SJP
• 0
0
votes
0
replies
75
views
Empty table plot using plotGseaTable()
FGSEA
1 hour ago by
Chris
▴ 260
0
votes
1
reply
121
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 1 day ago by
anovak
▴ 120 • written 1 day ago by
Hang
• 0
1
vote
3
replies
169
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
yvonneh
▴ 10
3
votes
5
replies
209
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
4 hours ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 1 day ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
132
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
1 day ago by
dtnondorf
• 0
0
votes
1
reply
160
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 19 hours ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
1
vote
2
replies
182
views
RNA-seq data for deep learning classification
rna-seq
10 hours ago by
yahn
• 0
2
votes
6
replies
285
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
22 hours ago by
Qroid
▴ 40
0
votes
1
reply
478
views
Loss of 'var' using concatenation of AnnData objects
Scanpy
AnnData
updated 1 day ago by
Hugo
• 0 • written 4 months ago by
Rachel
• 0
0
votes
1
reply
115
views
Provean help
variant
Provean
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Arun Sai Kumar
• 0
1
vote
1
reply
132
views
Download eQTL data of one specific gene for all tissues from GTEx
eQTL
GTEx
updated 1 day ago by
bk11
★ 2.4k • written 1 day ago by
Jeol
▴ 20
1
vote
1
reply
141
views
Super ehancers
enhancers
updated 1 day ago by
jared.andrews07
★ 16k • written 1 day ago by
Oburah
• 0
0
votes
6
replies
249
views
How does gene length effect the number of reads mapped
RNA-seq
CPM
sequencing
updated 8 hours ago by
dsull
★ 6.0k • written 1 day ago by
Chen
• 0
5
votes
5
replies
228
views
Problem with data downloaded from Short Reads Archive (SRA)
SRA
DADA2
metabarcoding
updated 1 day ago by
atharvakarkare14
▴ 30 • written 1 day ago by
Begonia_pavonina
▴ 150
1
vote
7
replies
412
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
11 hours ago by
eebloom
▴ 80
3
votes
3
replies
271
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 13 hours ago by
ATpoint
82k • written 1 day ago by
alifafiq1
• 0
0
votes
0
replies
89
views
Use of annotation of integrated Seurat object in single sample
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
96
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
116,750 results • Page
1 of 2335
Recent Votes
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
Greatly speed up conda by using mamba
Comment: Converting CRAM to FastQ
Parametric or non-parametric tests for qPCR significance testing between treatments?
Answer: Converting CRAM to FastQ
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Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
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Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
Yes, but I think the problem is what to do when MAF = 0.5
Answer: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In Plink, A1 is usually a minor allele and A2 a major allele. .frq (basic allele frequency report) Produced by --freq. …
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