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1,042 results • Page
4 of 21
Sort: Votes
Rank
Views
Votes
Replies
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 17 days ago by
Dr.Animo
▴ 130 • written 12 months ago by
BioinfoBee
• 0
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 24 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
4
votes
5
replies
550
views
Getting refseq assembly accession numbers from list of species names
haystac
accession
refseq
assembly
ncbi
updated 29 days ago by
GenoMax
142k • written 29 days ago by
Kuldeep
• 0
4
votes
4
replies
441
views
How do I install plink2 on a mac?
plink2
plink
updated 19 days ago by
zx8754
11k • written 22 days ago by
emilija.romic
▴ 10
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 4.8 years ago by
Rimma
▴ 30
4
votes
3
replies
10k
views
short and long reads
long-reads
Assembly
short-reads
updated 28 days ago by
Ram
43k • written 10.0 years ago by
midox
▴ 290
4
votes
4
replies
352
views
How to fetch published paper of a BioProject
BioProject
pumbed
NGS
25 days ago by
Morteza
• 0
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 1 day ago by
ST
• 0 • written 2.2 years ago by
Federico
• 0
4
votes
7
replies
706
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 7 days ago by
dsull
★ 6.0k • written 11 days ago by
qudrat.nii
▴ 10
4
votes
4
replies
390
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 22 days ago by
colindaven
6.4k • written 4 weeks ago by
Md Moinuddin
• 0
4
votes
4
replies
495
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 22 days ago by
damian.szk
▴ 80 • written 23 days ago by
rohitsatyam102
▴ 850
4
votes
3
replies
367
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 6 days ago by
Arup Ghosh
3.2k • written 7 days ago by
chaco001
▴ 40
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 19 days ago by
GenoMax
142k • written 15 months ago by
Estefania
▴ 30
3
votes
3
replies
297
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 1 day ago by
ATpoint
82k • written 2 days ago by
alifafiq1
• 0
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 17 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic
Gene-Ontology
GO
updated 23 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 9 days ago by
sp
• 0 • written 22 months ago by
Dan
▴ 180
3
votes
7
replies
980
views
How much adapters is it ok to keep in my samples after RNA seq?
RNA-seq
illumina
adapters
updated 29 days ago by
Ram
43k • written 5 months ago by
bioinfo
▴ 150
3
votes
3
replies
337
views
Visualize pathways from MSigDB
MSigdb
28 days ago by
Chris
▴ 260
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 16 days ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 17 days ago by
Ram
43k • written 4.7 years ago by
rodguinea
• 0
3
votes
8
replies
1.3k
views
Cellranger count error: Input FASTQ file ended prematurely
scRNA-seq
Cellranger
STARsolo
10X
updated 14 days ago by
swbarnes2
14k • written 9 months ago by
bp22
▴ 80
3
votes
3
replies
557
views
Korean human genome reference file
GWAS
reference
imputation
15 days ago by
SeoGyun
• 0
3
votes
4
replies
400
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 21 days ago by
Pierre Lindenbaum
161k • written 21 days ago by
Sony
▴ 10
3
votes
3
replies
320
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 18 days ago by
GenoMax
142k • written 18 days ago by
lorena9132
• 0
3
votes
5
replies
1.3k
views
NextGen Sequencing Folks, what do you keep as your raw backup? BCL's or FASTQ's? Both?
next-gen-sequencing
backups
data-storage
updated 28 days ago by
Ram
43k • written 2.2 years ago by
msn
▴ 130
3
votes
3
replies
515
views
Free/open source 23andme-like analysis
SNPs
genomics
NGS
VCF
updated 14 days ago by
swbarnes2
14k • written 15 days ago by
noodle
▴ 580
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 17 days ago by
Ram
43k • written 5.5 years ago by
prekrish
• 0
3
votes
2
replies
354
views
kraken2 vs krakenuniq
KrakenUniq
kraken2
28 days ago by
pinheirofabiano
▴ 20
3
votes
3
replies
642
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression
TCGA
miRNA
updated 24 days ago by
Ram
43k • written 5 months ago by
mohammadhassanj
▴ 260
3
votes
7
replies
545
views
Artificial deletion in bam
bam
updated 29 days ago by
Zhenyu Zhang
★ 1.2k • written 29 days ago by
enee
▴ 10
3
votes
5
replies
603
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align
RNA-Seq
linux
STAR
12 days ago by
n_navy
• 0
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma
differential-gene-expression
RNA-Seq
deseq2
updated 24 days ago by
Ram
43k • written 6.2 years ago by
firestar
★ 1.6k
3
votes
4
replies
425
views
Genome completeness and contamination: CheckM vs CheckM2
genome-completeness
contamination
29 days ago by
beacamara
• 0
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 15 days ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
2
replies
4.2k
views
Batch effects in sequencing data
batch-effect
updated 15 days ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
5
replies
260
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
21 hours ago by
Maverick
▴ 10
3
votes
5
replies
204
views
Generating mpileup file using samtools
mpileup
samtools
updated 1 day ago by
Joe
21k • written 1 day ago by
Ruqaiya
• 0
3
votes
1
reply
618
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 16 days ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
3
votes
4
replies
710
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
12 days ago by
rahu
• 0
3
votes
7
replies
342
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
4 days ago by
salias
• 0
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 16 days ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
3
votes
1
reply
2.2k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression
EdgeR
DESeq2
updated 24 days ago by
Ram
43k • written 8.1 years ago by
rieza.aprianto
▴ 10
3
votes
2
replies
313
views
Seeking Guidance on How to Annotate Unusual Cell Populations in Single-Cell Data
Transcriptomics
Single-Cell
updated 28 days ago by
Ram
43k • written 9 weeks ago by
Daddy
▴ 20
3
votes
3
replies
356
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
23 days ago by
george
• 0
3
votes
1
reply
278
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 22 days ago by
Ram
43k • written 22 days ago by
rj.rezwan
• 0
3
votes
4
replies
490
views
biomaRt error for different R version
biomaRt
R
updated 16 days ago by
GenoMax
142k • written 17 days ago by
manaswwm
▴ 510
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 7 days ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
3
votes
3
replies
252
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 12 days ago by
GenoMax
142k • written 12 days ago by
Mariana
▴ 40
3
votes
3
replies
324
views
How do I find up-to-date gene symbols for outdated names
names
symbols
gene
27 days ago by
DSmith
• 0
1,042 results • Page
4 of 21
Recent Votes
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Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
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This the tool still problematic?
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Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
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You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
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The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
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