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121,962 results • Page
198 of 2440
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3
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2
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822
views
how count different unique letter for each column?
R
updated 24 months ago by
Ram
45k • written 24 months ago by
star
▴ 350
1
vote
2
replies
1.5k
views
Hifiasm coverage rd:i:0
hifiasm
genome
coverage
assembly
24 months ago by
ccruz
• 0
2
votes
4
replies
1.9k
views
Query regarding genome coverage in de-novo assembly
genomics
Illumina
Novaseq
24 months ago by
microorganism_001
▴ 30
2
votes
3
replies
1.0k
views
How would you define homologous windows between 2 genomes?
genomics
comparison
mapping
24 months ago by
Axzd
▴ 80
0
votes
1
reply
672
views
how calculate different amino acids in a aligning format?
R
updated 24 months ago by
Ram
45k • written 24 months ago by
star
▴ 350
0
votes
3
replies
1.9k
views
Phyloseq and ASV names between datasets
dada2
phyloseq
16S
asv
updated 24 months ago by
antonioggsousa
3.4k • written 24 months ago by
pablo
▴ 350
2
votes
4
replies
1.2k
views
Super long time when running RSoptSC package
RSoptSC
single-cell
24 months ago by
alwayshope
▴ 40
4
votes
7
replies
1.5k
views
Alternative for grep in a for loop
linux
updated 24 months ago by
Ram
45k • written 24 months ago by
Prangan
▴ 20
1
vote
4
replies
1.4k
views
Plotting gene Expression per pathway
GO-enrichment
gene-expression
R
ggplot
RNA-seq
24 months ago by
Assa Yeroslaviz
★ 1.9k
2
votes
4
replies
1.4k
views
Can't find a gene in single cell
single-cell
24 months ago by
Chris
▴ 360
0
votes
1
reply
883
views
Help with DESeq2 Analysis of Multiple Conditions
DESeq2
updated 24 months ago by
Ram
45k • written 24 months ago by
Max
• 0
0
votes
0
replies
696
views
Forum:
Automated Checks And QA
retrospective
24 months ago by
Sasha
▴ 850
1
vote
3
replies
930
views
GSEA analysis for phosphoproteins
GSEA
updated 24 months ago by
dsull
★ 7.7k • written 24 months ago by
Tarana
• 0
0
votes
0
replies
485
views
Kobas-i metabolic pathways
metabolic-pathway-enrichment
kobas
updated 24 months ago by
Ram
45k • written 24 months ago by
bsp017
▴ 50
0
votes
4
replies
1.5k
views
Picard Liftover MismatchedRefAllele PsychArray
picard
24 months ago by
Eve
• 0
0
votes
4
replies
2.1k
views
Converting GFF to GTF
gff
gtf
updated 24 months ago by
Ram
45k • written 24 months ago by
Morgan
• 0
0
votes
0
replies
406
views
Calculating % CN-LOH for Illumina Microarray samples on genotyping array Global Diversity
LOH
24 months ago by
emily.walker
• 0
1
vote
1
reply
726
views
How to trim bases with bbduk.sh
bbmap
fastq
updated 24 months ago by
Ram
45k • written 24 months ago by
shivangi.agarwal800
▴ 120
2
votes
3
replies
3.4k
views
GENE ONTOLOGY FOR TOMATO-ITAG4.1 OR 4
BUILD
GO
ITAG4.1
SL4.0
updated 16 months ago by
Hamtaro
▴ 60 • written 2.9 years ago by
anusha
▴ 10
0
votes
9
replies
2.2k
views
Alignment of mirna on specific organism data from mirbase
mirbase
miRNA
updated 24 months ago by
Pierre Lindenbaum
166k • written 24 months ago by
otieno43
▴ 40
0
votes
1
reply
692
views
Copy Number Analysis of Multiple Cohorts Using CNVkit
CNVkit
updated 24 months ago by
rbioinfo
▴ 40 • written 24 months ago by
weisong
• 0
0
votes
4
replies
1.2k
views
Summit Extension in Cut&tag analysis
macs2
CHIP-seq
CutAndTag
motif
updated 24 months ago by
Ram
45k • written 24 months ago by
black_blue
• 0
4
votes
14
replies
8.4k
views
SRR download using fasterq-dump
GEO
SRR
24 months ago by
Biomed-jeh
▴ 70
1
vote
0
replies
584
views
Inconsistencies and QQ plot inflation in CMH Test Results for case-control Pool Seq: Underestimating Geographical Effects?
QQ-plot
CMH-test
Pool-Seq
24 months ago by
C
▴ 10
0
votes
4
replies
1.3k
views
Should I normalise RNA-seq data with this QC profile?
seqmonk
rna-seq
qc
normalisation
updated 24 months ago by
1769mkc
★ 1.3k • written 24 months ago by
a_bis
▴ 40
1
vote
3
replies
1.2k
views
combinations of biomarkers
machine-learning
biomarkers
24 months ago by
sil_bioinfo
▴ 60
4
votes
3
replies
1.4k
views
Over Representation analysis altered pathways in common between comparisons plot
R
Visualization
DGE
ORA
updated 24 months ago by
Basti
★ 2.1k • written 24 months ago by
Manuel
▴ 10
0
votes
2
replies
1.2k
views
Does ploidy in variant calling affect admixture detection with TreeMix?
ploidy
admixture
SNP
TreeMix
24 months ago by
Michael
56k
0
votes
0
replies
499
views
processing and downstream analysis of mzxml files in R
Proteomics
mzXML
24 months ago by
1769mkc
★ 1.3k
6
votes
2
replies
3.2k
views
how to make a UpSet plot with data frame in R
R
UpSet-plot
updated 24 months ago by
Ram
45k • written 2.4 years ago by
sata72
• 0
0
votes
2
replies
973
views
Reaction enrichment analysis
reaction-enrichment
GO
24 months ago by
dalibenam64
• 0
0
votes
7
replies
1.4k
views
create an all against all fasta file
python
fasta
updated 24 months ago by
Ram
45k • written 24 months ago by
Chu
• 0
3
votes
5
replies
1.9k
views
I have a pair of read files where each is a mixed pool of reads from the Linked-read technology and Illumina short-read technology. Any suggestion on…
NGS
clc-genomics
illumina
WGS
updated 24 months ago by
Ram
45k • written 24 months ago by
Vijith
▴ 100
0
votes
1
reply
819
views
chi-square test using vectors - and trying to for loop
R
chi-square
updated 24 months ago by
Ram
45k • written 24 months ago by
ohtang7
▴ 40
1
vote
1
reply
548
views
Create seurat inputs without cellranger
Seurat
updated 24 months ago by
Ram
45k • written 24 months ago by
ankit.yadav
• 0
1
vote
2
replies
706
views
lncRNA length in GENCODE gtf
lncRNA
24 months ago by
ziyan
• 0
0
votes
1
reply
1.4k
views
News:
FINAL CALL: Online Course - A Practical Introduction to NGS Data Analysis - October 23-25, 2023
DNA-seq
Workshop
RNA-seq
24 months ago by
David Langenberger
11k
0
votes
3
replies
1.0k
views
What is a tool to get the genome build of a VCF?
bcftools
vcf
updated 24 months ago by
Ram
45k • written 24 months ago by
a5864557
▴ 10
3
votes
7
replies
2.1k
views
Extract compounds/proteins from genomic data
plants
annotations
updated 24 months ago by
Mark
★ 1.7k • written 2.3 years ago by
Sorin
• 0
1
vote
2
replies
984
views
Does Beagle use VCF information such as the "GQ" value, depth, or similar?
imputation
vcf
beagle
24 months ago by
a5864557
▴ 10
0
votes
2
replies
1.5k
views
UniRef90 to UniRef50 conversion
Uniref
uniprot
updated 24 months ago by
yl759
▴ 120 • written 24 months ago by
Deep
• 0
0
votes
2
replies
1.1k
views
How to read tsv data as dgcmatrix
scRNA-seq
seurat
updated 24 months ago by
Ram
45k • written 24 months ago by
Alex
▴ 20
1
vote
1
reply
733
views
Trimmomatic
Trimmomatic
updated 24 months ago by
Ram
45k • written 24 months ago by
pradipnile4
• 0
1
vote
1
reply
878
views
Visualization of Genomes
genome
updated 23 months ago by
Ram
45k • written 24 months ago by
usman
• 0
1
vote
1
reply
601
views
Adaptive Sampling in NGS
NGS
updated 24 months ago by
GenoMax
154k • written 24 months ago by
pradipnile4
• 0
3
votes
4
replies
2.1k
views
Kallisto abundance.tsv
Kallisto
updated 24 months ago by
Ram
45k • written 24 months ago by
san96
▴ 190
0
votes
3
replies
1.7k
views
DESeq2: DESeqDataSetFromMatrix Error
R
RNA-seq
DESeq2
updated 24 months ago by
Ram
45k • written 24 months ago by
Athena
• 0
5
votes
6
replies
5.8k
views
How To Find The Enriched Repeat Elements Between Two Sequences
repeats
sequence
enrichment
updated 24 months ago by
guliar
• 0 • written 13.6 years ago by
Free Man
▴ 180
1
vote
3
replies
1.7k
views
pyDESeq2 Index Error?
R
python
pyDESeq2
DESeq2
24 months ago by
Emily
▴ 70
0
votes
1
reply
714
views
ChIP-seq peaks annotation
ChIP-seq
updated 24 months ago by
Ram
45k • written 24 months ago by
Maurice
• 0
121,962 results • Page
198 of 2440
Recent Votes
A: Which is the proper RNA-seq count table transformation to perform hierarchial cl
Answer: Differences between published differential gene expression results and own analy
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: If TPM is not comparable across cohorts, can it be used as the input for ML mode
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere
sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
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Recent Replies
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
If those logFCs are different, then that's a normalization issue. The logFC is straight forward arithmetic (it's simply dividing mean of […
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Thanks both for your input. It got me to look at the published methodologies more closely, and you guys were right. One paper that I was re…
Comment: Differences between published differential gene expression results and own analy
by
vernonlim98
• 0
Yes it does not match at all, and those genes that are common in both analysis results have very different logFC and p values
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
I am not sure what you mean by this, but I believe that is what I did. With Trinity, I matched all the paired reads together, so they shoul…
Answer: Gene expression equivalent of polygenic risk score ?
by
GouthamAtla
12k
I don't think something exists out of the box. With variants, we have a 'weight' for each variant on disease risk (obtained through large s…
Comment: ESTIMATE (Estimation of STromal and Immune cells in MAlignant Tumor tissues usin
by
Ben
• 0
write.table(df1, "df1.txt", sep = "\t", row.names = T, col.names = T, quote = FALSE)
Comment: Errors with RSEM/bowtie2
by
GenoMax
154k
That is good confirmation. Bacl to the error message. > I don't know how to fix this, given that I already did the trimming steps. DId yo…
Comment: Differences between published differential gene expression results and own analy
by
dsull
★ 7.7k
Honestly, those things shouldn't result in a considerable discrepancy. The largest difference will come from the post-processing & analysi…
Answer: Differences between published differential gene expression results and own analy
by
Ales
▴ 50
I second the comment about comparing the top 100 genes - if you see vastly different results, I would lean closer to examining protocols th…
Answer: Help interpreting BLASTn results and phylogenetic tree for genetics practical
by
Mensur Dlakic
★ 30k
I think what you are asking involves too much work for anyone to explain it in granular detail. But who knows, maybe there is a good soul o…
Answer: Differences between published differential gene expression results and own analy
by
yura.grabovska
▴ 830
When you say vastly different, what do you mean exactly? Does your top 100 up/down not match theirs at all?
Comment: Functional prediction for proteins of bacteria.
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colindaven
8.0k
Have a look at tools like SnpEff or Ensembl VEP. Perhaps your bacterial sp is included.
Comment: Errors with RSEM/bowtie2
by
Olivia
• 0
Yes, I already made the transcriptome with these tools, and the CD-HIT-EST fasta file is the transcript file that I am using for RSEM. Then…
Comment: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
by
Guilherme
• 0
Oh, ok. It seems like NCBI stores the files in SRA format (thus needing conversion and database lookups by sra toolkit tools) and EBI store…
Comment: help with modkit on nanopore sequencing data.
by
andres.firrincieli
3.9k
On the DMR tutorial page, they retrieve Human CpG Islands from the UCSC Table Browser. You can do the same thing for Mouse CpG Islands. Hav…
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