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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
172
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential
visualization
RNASeq
analysis
expression
enrichment
4 days ago by
Mark
• 0
0
votes
0
replies
159
views
busco id description
OrthoDB
BUSCO
updated 4 days ago by
Ram
39k • written 4 days ago by
angelina
• 0
0
votes
5
replies
389
views
how to Construct a Newick tree file from five large fasta files
tree
Newick
alignment
updated 4 days ago by
Joe
21k • written 5 days ago by
gunala.nikhil
• 0
0
votes
0
replies
164
views
NMDS plotting issue
NMDS
metagenomic
4 days ago by
arshad1292
▴ 90
0
votes
2
replies
239
views
featurecounts not working on mirbase annotation file
usegalaxy
miRNA-seq
1 day ago by
demoraesdiogo2017
▴ 90
0
votes
0
replies
142
views
IGV insertions
insertions
IGV
5 days ago by
christoph.schubart
• 0
1
vote
0
replies
154
views
Bayesian network for biological data using bnlearn
bnlearn
RNA-seq
bayesian-network
updated 4 days ago by
Ram
39k • written 5 days ago by
priyankamehta.1811
▴ 10
0
votes
0
replies
148
views
jellyfish options
kmer
jellyfish
5 days ago by
Tele
• 0
0
votes
3
replies
227
views
hardfilter error
bam
recall
5 days ago by
bestone
▴ 10
0
votes
0
replies
124
views
cnetplot enrichment graph to cytoscape
clusterprofiler
cnetplot
enrichplot
5 days ago by
Omics data mining
▴ 220
0
votes
0
replies
125
views
How to extract the surrogate variables from DNA methlation Data
sva
array
limma
methylation
updated 5 days ago by
GenoMax
129k • written 5 days ago by
Dablax
• 0
1
vote
1
reply
599
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap
Nanopore
IGV
updated 5 days ago by
GenoMax
129k • written 5 days ago by
Mohd
▴ 20
0
votes
0
replies
116
views
Convert tree into bifurcation table
Tree
Newick
ASR
Mutation
5 days ago by
Alexandre
• 0
0
votes
1
reply
185
views
Processing WES VCF for case control GWAS analysis
GWAS
PLINK
updated 5 days ago by
raphael.B
▴ 360 • written 5 days ago by
sonsunjirachote
• 0
4
votes
6
replies
1.5k
views
Why weblogo of biopython doesn't work?
Biopython
Weblogo
updated 5 days ago by
minakshiboruahassam
• 0 • written 9 months ago by
Plus
▴ 20
1
vote
2
replies
227
views
The famous WGS dataset, Ashkenazi Trio?
wgs
dataset
updated 4 days ago by
thadjudkins2
• 0 • written 5 days ago by
herh
• 0
1
vote
0
replies
143
views
Integrating mRNA and microRNA analysis results
mRNA
microRNA
5 days ago by
abba647
▴ 10
4
votes
4
replies
293
views
Does adding reads cause batch effects?
kallisto
RNAseq
updated 5 days ago by
ATpoint
72k • written 5 days ago by
bioinfo
▴ 80
0
votes
1
reply
165
views
Merge different vcf files
vcf
updated 4 days ago by
Ram
39k • written 5 days ago by
caique.manochio
• 0
0
votes
4
replies
279
views
Identification of genes involved in my pathway
KEGG
keggGet
5 days ago by
smanzano250800
• 0
0
votes
8
replies
348
views
The inchworm process failed. Trinity running error.
inchworm
transcriptome
trinity
updated 5 days ago by
GenoMax
129k • written 6 days ago by
Marta
• 0
1
vote
2
replies
209
views
Combination of ROC CURVE
roccurve
R
AUC
2 days ago by
Maria17
▴ 20
1
vote
0
replies
97
views
Considering gaps in calculating conservation score from MSA
multiple
alignment
sequence
conservation
python
6 days ago by
Jonathan Lefebre
▴ 70
0
votes
3
replies
180
views
DEGseq for multiple samples
DEGseq
DEG
updated 5 days ago by
Ram
39k • written 6 days ago by
ALOUSH ALI
• 0
0
votes
0
replies
80
views
Metabolomics Data Annotation
annotation
metabolomics
camera
updated 5 days ago by
Ram
39k • written 6 days ago by
Rishabh Jha
• 0
1
vote
3
replies
210
views
My kernel is killing the pairtools dedup script, how to prevent that?
ubuntu
hic
pairtools
aws
updated 5 days ago by
GenoMax
129k • written 6 days ago by
NikhilP
▴ 20
2
votes
2
replies
182
views
bioinformatic analysis protocol performed by CD Genomics
Genomics
analysis
CD
Protocol
updated 20 hours ago by
Ram
39k • written 6 days ago by
linnet.roque6
▴ 10
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by
Pegasus
▴ 90 • written 3.7 years ago by
mnazir
▴ 10
0
votes
0
replies
106
views
RRBS fastq - biased per base sequence content
fastqc
rrbs
6 days ago by
mbk0asis
▴ 670
0
votes
0
replies
303
views
What are the existing proposals for how to approach genomic coordinates in a pangenome reference environment?
coordinates
pangenome
genomic
6 days ago by
Vincent Laufer
★ 2.9k
0
votes
0
replies
106
views
Determining Cutoff for score in a bed file in ATAC-seq Data Analysis
bed
ATAC-seq
updated 6 days ago by
Ram
39k • written 6 days ago by
Mah
• 0
1
vote
3
replies
221
views
To call variants can I use my aligned WGS data as a reference genome
VCF
samtools
reference
genome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
mls
• 0
0
votes
0
replies
109
views
snpEff error. No CDS checked
snpEff
gtf
WES
6 days ago by
fifty_fifty
▴ 40
0
votes
0
replies
111
views
Tool to align metagenomic data to reference genome
tool
metagenomics
alignment
6 days ago by
Maddie
• 0
1
vote
2
replies
209
views
how to look for interactions between different chromosomes
SNP
interactions
Gene
HiC
5 days ago by
rheab1230
▴ 140
2
votes
4
replies
239
views
Filter VCF file for variant alleles
VCF
variants
bcftools
vcftools
updated 6 days ago by
Ram
39k • written 6 days ago by
miguellarrazlopezdenovales
• 0
1
vote
0
replies
107
views
Linear models with limma: coefficients not estimatable, are the others OK?
limma
6 days ago by
fr
▴ 200
0
votes
2
replies
175
views
Ambient RNA expression correction
scRNAseq
SoupX
Seurat
updated 6 days ago by
rpolicastro
12k • written 6 days ago by
Pac314
▴ 10
0
votes
2
replies
167
views
readGenericHeader() error message Limma
rna
limma
microarray
genomics
normalization
6 days ago by
survive
• 0
1
vote
1
reply
129
views
mitochondrial genome, SRA PacBio sequencing.
Mitochondrial
PacBio
SRA
Mitogenome
updated 6 days ago by
GenoMax
129k • written 6 days ago by
hashim.rana11
▴ 20
0
votes
0
replies
80
views
metagenomics data - AMR genes
amr
resistome
resistance
ARG
metagenomics
7 days ago by
aziznasr1920
▴ 10
1
vote
3
replies
190
views
How to get a comperative result of 2 bed files?
bam
cnv
bed
updated 6 days ago by
Pierre Lindenbaum
154k • written 7 days ago by
herh
• 0
0
votes
0
replies
75
views
1000G reference panel for LD clumping
LD
7 days ago by
en_keser
• 0
0
votes
0
replies
85
views
Nucleotide alignments from mmseqs "tblastn"
mmseqs2
tblastn
mmseqs
7 days ago by
saladi
▴ 30
0
votes
2
replies
612
views
ERROR running Cuffmerge in reference based RNA-SEQ analysis?
cuffmerge
RNA-Seq
Cufflinks
updated 7 days ago by
Ram
39k • written 13 months ago by
Meeran
• 0
0
votes
7
replies
578
views
How to deal with duplicated gene IDs in TCGA RNA expression data?
TCGA
Expression
mRNA
updated 7 days ago by
Vincent Laufer
★ 2.9k • written 11 days ago by
Camilo Andres
▴ 30
0
votes
3
replies
210
views
Dada2 in Qiime2: losing reads during merging
Qiime2
Chimer
Dada2
updated 6 days ago by
andres.firrincieli
3.4k • written 7 days ago by
kamanovae
▴ 80
0
votes
1
reply
155
views
NCBI Common Taxonomy Tree
phylogenetic-tree
comparative-taxonomy
ncbi
updated 7 days ago by
GenoMax
129k • written 7 days ago by
fafad046
• 0
0
votes
3
replies
196
views
minimap's SAM file MAPQ value for the unique alignments
minimap
MAPQ
RNAseq
6 days ago by
Mohd
▴ 20
1
vote
2
replies
182
views
sorting BAM file
BAM
updated 7 days ago by
ATpoint
72k • written 7 days ago by
Mohammad Amin
• 0
1,000 results • Page
2 of 20
Recent Votes
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
A: Collapse Repeated Reads
A: Extract Reads From A Bam File That Fall Within A Given Region
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
Comment: Alignment of case vs. control from different origin
A: understanding bedtools coverage output
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lait
▴ 170
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GenoMax
129k
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blur
▴ 270
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Recent Replies
Comment: switching from illumination to NEB prep kits
by
GenoMax
129k
If you are simply replacing the library prep kit then it will be compatible with normal illumina libraries. If there is a different adapter…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Zhichao
• 0
yes, I have activated this conda environment. And the conda is in `PATH` . At first, I create a new conda environment `conda create -n ne…
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Raw counts, raw meaning not manipulated by any transformation. See limma and edgeR manual, it clearly covers that for using limma-trend and…
Comment: Alternative To interactions comparison in limma in DESeq2
by
ATpoint
72k
https://support.bioconductor.org/p/9143932/ -- see the lower parts where Michael Love answers, it comes down to numeric contrasts.
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
The `mat` is log2-normalized raw data. Is it feasible? Or should I feed in counts?
Comment: DESeq2 for different design and normalized counts
by
ATpoint
72k
Nope, please read the manual of DESeq2, it clearly tells to use raw counts. What "normalized counts" do you have exactly? limma-trend might…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
ATpoint
72k
Did you activate your conda environment? Is conda in `PATH`? Please describe what you did.
Comment: Limma returned only positive logFC values
by
ATpoint
72k
Bottom line is, if you are using an intercept-free model (that is what `~0+...` is doing) then you have to use contrasts. In a "normal" mod…
Comment: Asking for feedback on a Python library for computing alignments
by
Alexander
▴ 70
Thanks for sharing ! It seems there is a problem to install on Kaggle cloud (like a Colab): I tried several ways: https://www.kaggle.com/co…
Comment: Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
by
Darked89
4.4k
I am not sure what you gain by using hard masked genome for RNA-Seq mapping. There will be reads covering some introns. But if you mask rep…
Comment: Extract sequences from a fastq file by a list of IDs
by
mhpakdel96
• 0
Thanks a lot, it works
Comment: Differential protein expression analysis
by
dsull
★ 4.2k
I don't have a tutorial but see this paper I co-authored: https://pubs.acs.org/doi/abs/10.1021/acs.jproteome.0c00666 All of the upstream …
Comment: Differential protein expression analysis
by
Ribo
▴ 40
Thank you! Is there a recommended tutorial for proteomics analysis?
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
I clustered the samples into subtypes and am now comparing the differential expression across the subtypes.
Answer: Limma returned only positive logFC values
by
Gordon Smyth
★ 6.1k
No, your code isn't correct. You are testing one group mean equal to zero instead of testing for differences between two groups. I wonder w…
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