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996 results • Page
3 of 20
Sort: Votes
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Votes
Replies
5
votes
3
replies
740
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 18 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
2
replies
675
views
DESeq2- How to design data for multiple comparisons?
Differential-Gene-Expression
RNA-Seq
DESeq2
R
updated 28 days ago by
Ram
43k • written 3.6 years ago by
ginny
• 0
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts
DESEQ2
differential-gene-expression
kallisto
updated 28 days ago by
Ram
43k • written 2.8 years ago by
mrj
▴ 170
5
votes
3
replies
346
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 26 days ago by
cmdcolin
★ 3.8k • written 27 days ago by
William
★ 5.3k
5
votes
6
replies
1.8k
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 2 days ago by
MiladAD
▴ 10 • written 24 months ago by
soheil
• 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 28 days ago by
Ram
43k • written 6.5 years ago by
vikram
▴ 10
5
votes
4
replies
363
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
21 days ago by
Spring
• 0
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 28 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
5
votes
2
replies
1.1k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 21 days ago by
Ram
43k • written 3.8 years ago by
svp
▴ 680
5
votes
2
replies
311
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 8 days ago by
i.sudbery
19k • written 11 days ago by
vanbelj
▴ 40
5
votes
14
replies
1.0k
views
Not getting any modification calls in nanopore reads with dorado basecaller
mofications
dorado
basecalling
nanopore
methylation
updated 26 days ago by
GenoMax
142k • written 6 weeks ago by
njornet
▴ 20
5
votes
1
reply
121
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 11 hours ago by
Ram
43k • written 13 hours ago by
ijarne
• 0
5
votes
5
replies
572
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 28 days ago by
noodle
▴ 580 • written 29 days ago by
a615ebfb
▴ 40
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 21 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
5
votes
3
replies
415
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 26 days ago by
GenoMax
142k • written 26 days ago by
AHerik
▴ 20
5
votes
4
replies
386
views
Forum:
Ideal PC configurations and operating system for bioinformatics laboratory
PC
5 days ago by
Estevão
• 0
5
votes
5
replies
7.3k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 27 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
13
replies
1.6k
views
Tutorial:
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
R
Ubuntu
Linux
Bioconductor
Rstudio
updated 17 days ago by
ATpoint
82k • written 18 days ago by
BioinfGuru
★ 1.7k
5
votes
5
replies
606
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 4 days ago by
Mbofire
• 0 • written 13 days ago by
Ming Tommy Tang
★ 3.9k
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 7 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
4
votes
7
replies
594
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
8 days ago by
e.r.zakiev
▴ 210
4
votes
1
reply
322
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
8 days ago by
pairedttest
▴ 10
4
votes
7
replies
748
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 11 days ago by
dsull
★ 6.0k • written 15 days ago by
qudrat.nii
▴ 10
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
8 days ago by
anna
▴ 20
4
votes
1
reply
225
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 1 day ago by
zx8754
11k • written 3 days ago by
Jautis
▴ 560
4
votes
4
replies
395
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 25 days ago by
colindaven
6.4k • written 5 weeks ago by
Md Moinuddin
• 0
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 20 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
7
replies
558
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 12 days ago by
dsull
★ 6.0k • written 14 days ago by
VITALA
• 0
4
votes
5
replies
413
views
Figures are disappeared from html report of SnpEff
HTML
SnpEff
9 days ago by
analyst
▴ 30
4
votes
2
replies
423
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 12 days ago by
shalespringer
• 0 • written 12 weeks ago by
Phenylananin
▴ 20
4
votes
11
replies
838
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 14 days ago by
LauferVA
4.2k • written 15 days ago by
dominickd
• 0
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 28 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
4
votes
4
replies
456
views
How do I install plink2 on a mac?
plink2
plink
updated 22 days ago by
zx8754
11k • written 25 days ago by
emilija.romic
▴ 10
4
votes
6
replies
1.5k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 22 days ago by
GenoMax
142k • written 15 months ago by
Estefania
▴ 30
4
votes
0
replies
140
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
8 days ago by
Biostar
2.7k
4
votes
15
replies
1.6k
views
how to test for differential expression in samples where a global increase in gene expression is expected
edgeR
DESeq
Differential-Expression
RNA-Seq
updated 4 days ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
4
votes
9
replies
2.7k
views
Tool:
CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by
dvelmeshev
• 0
4
votes
6
replies
508
views
Odd results with BLAST remote
blast
remote
NCBI
updated 21 days ago by
b.contreras.moreira
▴ 180 • written 22 days ago by
Begonia_pavonina
▴ 150
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 20 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
13
replies
961
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 21 days ago by
BioinfGuru
★ 1.7k • written 26 days ago by
matteo.levorato
• 0
4
votes
2
replies
3.8k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 19 days ago by
Ram
43k • written 6.6 years ago by
georgewwp
▴ 30
4
votes
4
replies
355
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
28 days ago by
Morteza
• 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 21 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 28 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 29 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
9
replies
2.1k
views
6 follow
Same sequencing sample in multiple lanes. How to analyse it?
sequencing
bowtie2
alignment
samtools
ngs
updated 4 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
8
replies
722
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 11 days ago by
Alex Reynolds
35k • written 12 days ago by
J
▴ 10
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 28 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 1 day ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
4
votes
3
replies
386
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 10 days ago by
Arup Ghosh
3.2k • written 11 days ago by
chaco001
▴ 40
996 results • Page
3 of 20
Recent Votes
removeBatchEffect explained using base R linear models
Answer: ChIP-seq datasets: input samples omitted?
Answer: ChIP-seq datasets: input samples omitted?
Answer: Is therer any suggestions on mapping rate of WGBS data?
A: Download full list of SNPs and their coordinates in hg38
Answer: HCL database download
Answer: Tissue-specific DEG analysis with DEseq2
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Comment: High Malat-1 expression in single cell data
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Resolved by increasing heapsize of -Xmx50G
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Talk to your HPC sysadmin - array jobs might be getting different kinds of nodes compared to standalone jobs.
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Thank you for your answer!
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I solved the problem by conneting another internet exploer. I think it was probably a problem with Chrome itself.
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Hi, What protocol did you use for TCR-seq library preparation? Generally speaking, there is no need to remove barcodes, as MiXCR can work …
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I've implemented fm index with backward search and need an inexact search to implement on FM index, I couldn't understand how fm index coul…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
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The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
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You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
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Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
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After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
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Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
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Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
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The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
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See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
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