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962 results • Page
3 of 20
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Votes
Replies
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression
RNA-Seq
GTex
DESeq2
updated 26 days ago by
Ram
43k • written 6.5 years ago by
vikram
▴ 10
5
votes
13
replies
9.2k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 24 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva
combat
batch-effect
DESeq2
updated 18 days ago by
Ram
43k • written 3.8 years ago by
svp
▴ 680
5
votes
3
replies
281
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 5 days ago by
Lluís R.
★ 1.2k • written 5 days ago by
이민경[학생](대학원 융합의과학과)
• 0
5
votes
5
replies
569
views
NCBI MEGABLAST versus UCSC BLAT
blast
blat
alignment
megablast
updated 25 days ago by
noodle
▴ 580 • written 26 days ago by
a615ebfb
▴ 40
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq
bulk-RNASeq
RNA-Seq
single-cell
updated 24 days ago by
veldahan86
• 0 • written 3.8 years ago by
Assa Yeroslaviz
★ 1.8k
5
votes
5
replies
876
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 22 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
5
votes
4
replies
685
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
11 days ago by
kirillkirilenko
▴ 40
5
votes
20
replies
4.2k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression
RNA-seq
updated 26 days ago by
Ram
43k • written 6.2 years ago by
pablo61991
▴ 90
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 26 days ago by
Ram
43k • written 2.7 years ago by
mrj
▴ 170
5
votes
3
replies
734
views
Illumina reads preprocessing best practice for snp calling applications
Illumina
snp
updated 16 days ago by
Enrique
• 0 • written 9 months ago by
Denis
▴ 310
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 18 days ago by
Ram
43k • written 3.2 years ago by
Rob
▴ 170
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 15 days ago by
ATpoint
82k • written 16 days ago by
BioinfGuru
★ 1.7k
5
votes
5
replies
261
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
5
votes
3
replies
411
views
Ensembl assembly choice for DNA reference with no combined primary assembly
alignment
HISAT2
RNA-Seq
ensembl
Assembly
updated 23 days ago by
GenoMax
142k • written 23 days ago by
AHerik
▴ 20
5
votes
2
replies
1.8k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 18 days ago by
Ram
43k • written 3.0 years ago by
Mat
▴ 60
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression
RNA-Seq
deseq2
updated 26 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
4
votes
7
replies
4.6k
views
snakemake output directory
snakemake
ngs
updated 19 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 18 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
3
replies
371
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 7 days ago by
Arup Ghosh
3.2k • written 8 days ago by
chaco001
▴ 40
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 1 day ago by
Gordon Smyth
★ 7.1k • written 4 months ago by
raplayer
▴ 10
4
votes
0
replies
135
views
Herald:
The Biostar Herald for Monday, April 29, 2024
herald
6 days ago by
Biostar
2.7k
4
votes
13
replies
946
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 18 days ago by
BioinfGuru
★ 1.7k • written 24 days ago by
matteo.levorato
• 0
4
votes
7
replies
589
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
6 days ago by
e.r.zakiev
▴ 210
4
votes
2
replies
306
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
5 days ago by
pairedttest
▴ 10
4
votes
4
replies
442
views
How do I install plink2 on a mac?
plink2
plink
updated 20 days ago by
zx8754
11k • written 23 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 20 days ago by
GenoMax
142k • written 15 months ago by
Estefania
▴ 30
4
votes
6
replies
499
views
Odd results with BLAST remote
blast
remote
NCBI
updated 19 days ago by
b.contreras.moreira
▴ 180 • written 20 days ago by
Begonia_pavonina
▴ 150
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 26 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
4
replies
392
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 23 days ago by
colindaven
6.4k • written 4 weeks ago by
Md Moinuddin
• 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 5 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
4
votes
11
replies
814
views
Redirection of Duplicate PMIDs
pubmed
pmid
updated 11 days ago by
LauferVA
4.2k • written 12 days ago by
dominickd
• 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 17 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 18 days ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
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 2 days ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
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
2
replies
352
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 17 days ago by
Juke34
8.6k • written 17 days ago by
njornet
▴ 20
4
votes
2
replies
406
views
Missing protein (VEGF-A) in String db
VGFA
stringdb
updated 9 days ago by
shalespringer
• 0 • written 12 weeks ago by
Phenylananin
▴ 20
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 18 days ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
4
votes
4
replies
483
views
Error Codes in Snakemake
python
snakemake
29 days ago by
888pea
▴ 10
4
votes
2
replies
323
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 19 days ago by
Ram
43k • written 19 days ago by
Adi
▴ 10
4
votes
7
replies
715
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 8 days ago by
dsull
★ 6.0k • written 12 days ago by
qudrat.nii
▴ 10
4
votes
8
replies
673
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 8 days ago by
Alex Reynolds
35k • written 9 days ago by
J
▴ 10
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression
RNA-Seq
updated 26 days ago by
Ram
43k • written 5.5 years ago by
lkianmehr
▴ 100
4
votes
7
replies
590
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 21 days ago by
Ram
43k • written 22 days ago by
AHerik
▴ 20
4
votes
7
replies
519
views
To get p-values for the TPM
P-value
TPM
RSEM
updated 10 days ago by
dsull
★ 6.0k • written 11 days ago by
VITALA
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
5 days ago by
anna
▴ 20
4
votes
4
replies
496
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 23 days ago by
damian.szk
▴ 80 • written 24 days ago by
rohitsatyam102
▴ 850
4
votes
4
replies
352
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
26 days ago by
Morteza
• 0
4
votes
0
replies
882
views
Tool:
PyComplexHeatmap: a Python package to visualize multimodal genomics data
visualization
Python
ComplexHeatmap
PyComplexHeatmap
24 days ago by
Wubin
▴ 40
962 results • Page
3 of 20
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Answer: Association study using SNP data
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Overlap File for RACON Genome Polisher
Answer: LD-prune variants while maintaining a list of SNPs
Comment: TaxID mapping file
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Answer: install package
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▴ 10
One way might be to try and see if you can download and install the package tarball locally 1. Get the package tarball from CRAN Archive [I…
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by
MiladAD
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God bless you man.
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Hi, This is what happens when I run some code to diagnose the issue. First, I wanted to see what version of R was required for the package…
Comment: TaxID mapping file
by
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thank you, I'll look at these files/documents. .
Answer: LD-prune variants while maintaining a list of SNPs
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I was given a solution by a colleague -- it seems a little hacky, but worked really well! > one way to get this to work is to use --clu…
Answer: Association study using SNP data
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• 0
Hi Matthew, Thank you very much for your inputs. I am working with Neogen genotyping data, which includes GC values less than 0.15.
Comment: Downloading full alignments from Pfam
by
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I tried contacting Pfam, they replied that indeed there is an issue on their side with the full alignments, which should be repaired in the…
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Don't know about others, but I would never contact someone about potential employment based only on their interests and with zero knowledge…
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If you are talking about methylation idat files, they were all migrated from legacy to the data portal. If you are talking about other pl…
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These TCGA samples were taken 10 ~ 20 years ago, and there is no way they have been treated by the modern immunotherapy. Are you sure tha…
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> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
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lorena9132
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Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
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Mathew
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Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
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Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
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SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
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