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1,000 results • Page
1 of 20
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0
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6
views
want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs.
DEGs
updated 4 minutes ago by
ATpoint
68k • written 6 minutes ago by
rupali
• 0
0
votes
0
replies
16
views
RNA Editing data from RNA-seq
Editing
RNA
46 minutes ago by
Genetics
• 0
0
votes
2
replies
26
views
cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
bcl2fastq
cellranger-arc
mkfastq
cellranger
30 minutes ago by
Yingying
• 0
0
votes
0
replies
32
views
Unrooted consensus tree [Bio.Phylo]
consensus
phylo
biopython
2 hours ago by
Jimpix
▴ 10
0
votes
0
replies
24
views
PLINK2 selecting variants based on INFO score
plink2
3 hours ago by
m.c.roozen
• 0
0
votes
0
replies
30
views
What is the difference between gseapy.prerank and gseapy.gsea?
gseapy
gsea
4 hours ago by
bioinfo
▴ 20
3
votes
6
replies
133
views
Which file and data structure is used to create volcano plot from scRNA-Seq experiment?
plot
Volcano
2 hours ago by
Chris
▴ 60
0
votes
1
reply
54
views
Converting large GSM from GEOquery into a minfi or limma workable set
minfi
methylation
limma
GEOquery
R
updated 4 hours ago by
Basti
★ 1.3k • written 5 hours ago by
Edward E-B
• 0
1
vote
1
reply
60
views
bwa mem duration?
performance
mapping
bwa
updated 6 hours ago by
ATpoint
68k • written 6 hours ago by
lacb
▴ 30
0
votes
1
reply
87
views
Gene ontology with locus tags
ontology
locus
gene
tags
updated 5 hours ago by
dthorbur
▴ 260 • written 8 hours ago by
sea.joson
▴ 10
0
votes
1
reply
91
views
Clustering and dynamic tree cutting
dynamicTreeCut
Clustering
data
RNAseq
cutreeDynamic
updated 6 hours ago by
andres.firrincieli
3.1k • written 8 hours ago by
harish
• 0
0
votes
6
replies
195
views
STAR is running but .sam file size does not increase after hours mapping
STAR
RNA-seq
mapping
SAM
updated 6 hours ago by
GenoMax
125k • written 9 hours ago by
luzglongoria
▴ 40
0
votes
4
replies
193
views
HTSeq error processing GFF file
HTSeq
GFF
GTF
2 hours ago by
ibq.enriquepola
• 0
0
votes
0
replies
72
views
which tool to use for Transposon structure finding CENSOR or repeat masker ??
transposon
DNA
repeat
CENSOR
masker
15 hours ago by
manaswiniparija3
▴ 10
0
votes
0
replies
76
views
scATAC merging of files
Signac
scATAC-seq
18 hours ago by
bioinformatics.girl
• 0
0
votes
0
replies
86
views
what does ALT ID DUP refer to when ALT ID for copy number are already specified
ALT
ID
CNV
VCF
20 hours ago by
anubratadas
▴ 20
0
votes
0
replies
108
views
How to use gseapy after scanpy?
gsea
single
cell
enrichR
gseapy
4 hours ago by
bioinfo
▴ 20
0
votes
0
replies
91
views
VNTR genotyping
NGS
VNTR
genotyping
21 hours ago by
Genotepes
▴ 950
0
votes
0
replies
85
views
Which AF column do I use from TCGA data in maftools
vcf2maf
sequencing
genome
WES
maf
22 hours ago by
CH1374
▴ 10
0
votes
0
replies
81
views
Chloroplast genome phylogenetic analysis
Inverted
region
Chloroplast
genome
Phylogenetic
analysis
SSC
22 hours ago by
a.bibek52
• 0
0
votes
0
replies
81
views
mVISTA annotation
alignment
Annotation
S-LAGAN
mVISTA
22 hours ago by
a.bibek52
• 0
2
votes
2
replies
169
views
Analyzing bulk RNA-seq
RNAseq
updated 21 hours ago by
swbarnes2
13k • written 1 day ago by
Zaid
• 0
1
vote
13
replies
309
views
RNAseq for DE purpose
RNAseq
updated 21 hours ago by
swbarnes2
13k • written 1 day ago by
m.habib
• 0
0
votes
0
replies
76
views
Identifying off-target mutation frequency in Bacterial genomes
dCas9-deaminase
off-target
SNPS
WGS
dCas9
1 day ago by
pd378
• 0
0
votes
0
replies
70
views
SVA correction reduces ability to detect genes as differential expressed?
effects
RNAseq
expression
batch
SVA
gene
1 day ago by
MB
▴ 50
0
votes
7
replies
307
views
CoveragePlot in Signac from MACS2 Object
Signac
scATAC-seq
updated 4 hours ago by
seidel
10k • written 1 day ago by
bioinformatics.girl
• 0
0
votes
1
reply
126
views
Remove duplicates in multifasta, where entries are paired
bash
python
updated 4 hours ago by
dthorbur
▴ 260 • written 1 day ago by
SaltedPork
▴ 170
1
vote
1
reply
116
views
snakemake Unexpected keyword bam in rule definition
snakemake
updated 1 day ago by
Ram
37k • written 1 day ago by
Aidand
• 0
0
votes
0
replies
76
views
Normalize Together Total RNA-SEQ vs Ampliseq protocols reads
RNA-seq
deseq2
ampliseq
ion-torrent
R
1 day ago by
Fernando
• 0
0
votes
0
replies
78
views
Combining mRNA and total RNA studies
RNA-Seq
bulk
updated 1 day ago by
Ram
37k • written 1 day ago by
aksh
• 0
0
votes
0
replies
70
views
Twist Exome Sequencing Data: Palindromic Tandem Insertion-Deletion
NGS
Artefact
Twist
Sequencing
Exome
1 day ago by
TraPS-VarI
• 0
0
votes
0
replies
127
views
Bootstrap in PhyML
phyml
bootstrap
1 day ago by
Jimpix
▴ 10
0
votes
0
replies
109
views
Cibersort phenotpe file to create signature matrix
deconvolution
cibersort
file
phenotype
1 day ago by
ce810b57
• 0
0
votes
0
replies
121
views
Enrichment map in python/ Pathway network by using python
interaction.
enrichment
network
pathway
analysis
1 day ago by
sonsunjirachote
• 0
0
votes
1
reply
163
views
How to analysis genomes with orthologs?
ortholog
genome
annotation
updated 1 day ago by
GenoMax
125k • written 1 day ago by
沛煒
• 0
0
votes
0
replies
108
views
Does the falcon input CLR reads need corrected by Canu?
Genome
assemble
1 day ago by
leeunfeng
• 0
0
votes
0
replies
95
views
CUT&RUN H3K27me3 normalization with spike-in
deepTools
1 day ago by
mohansri1
• 0
0
votes
0
replies
109
views
How to identify nodes in a network with a higher degree and higher edge variance?
network
variance
WGCNA
igraph
updated 1 day ago by
ATpoint
68k • written 1 day ago by
adR
▴ 100
0
votes
2
replies
179
views
Can you apply Base Score Recalibration in parallel?
wgs
updated 1 day ago by
LChart
1.8k • written 2 days ago by
optimistsso4co3
▴ 100
0
votes
3
replies
245
views
Change accession number to chromosome number in reference genome
fasta
chromosome
updated 1 day ago by
Ram
37k • written 2 days ago by
Tsigabu
• 0
0
votes
0
replies
83
views
Median depth across samples from multi-sample VCF
DP
bcftools
2 days ago by
alex.blakes
• 0
0
votes
5
replies
232
views
Add Information to Protein Fasta Headers
protein
fasta
functional-annotation
header
1 day ago by
ahmadjoyyia
• 0
3
votes
2
replies
161
views
WGCNA gene selection: gene significance or LASSO?
LASSO
WGCNA
updated 1 day ago by
rpolicastro
11k • written 2 days ago by
janinubinu
• 0
0
votes
0
replies
84
views
count_matrix.csv generated by "prepDE.py3" script in Python3
Stringtie
RNA-seq
1 day ago by
Pegasus
▴ 40
0
votes
3
replies
258
views
biological vs. technical definition of "insert size"
grinder
simulated-reads
shotgun-sequencing
updated 1 day ago by
ATpoint
68k • written 2 days ago by
sovrappensiero
▴ 50
0
votes
0
replies
77
views
Haloplex HS - should you remove duplicates?
deduplicate
Haloplex
duplicates
2 days ago by
amy__
▴ 50
0
votes
0
replies
83
views
Interpreting SnpEff output plots
NGS
Annotation
SnpEff
WGS
WES
2 days ago by
Alireza
▴ 20
0
votes
0
replies
76
views
Using DANPOS2 to determine nucleosome positions
MNase-seq
DANPOS
ENCODE
bigwig
2 days ago by
elisheva
▴ 120
0
votes
0
replies
82
views
How to determine the receptor and binding site of a protein transcribed from a gene
gene
2 days ago by
yoser4
▴ 10
0
votes
3
replies
156
views
blast engine error empty blast query vector
error
alignment
Blast
updated 2 days ago by
pbioinf
▴ 30 • written 2 days ago by
Sowmya Pulapet
▴ 10
1,000 results • Page
1 of 20
Recent Votes
Comment: RNA seq analysis from the data file which received from company
Answer: Multiple sequence alignment of sequenecs of different length
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
Comment: Alien-hunter outputs
Answer: Annotating ENS codes to gene name
Comment: Annotating ENS codes to gene name
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Recent Replies
Comment: want the codes for Deseq2 to perform DEGs.
by
rupali
• 0
thanks for help
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
Yingying
• 0
Hi, Yes I've uploaded the diagnostic file to 10x support already, but haven't got any response yet.
Comment: cellranger-arc mkfastq Error: bcl2fastq was killed with signal -11
by
GenoMax
125k
You may want to contact 10x tech support. When this process failed it must have created a diagnostic archive. You also get a message about …
Answer: How to merge unique/non overlapping genes between 2 gene model GFF3 files?
by
jv
▴ 780
`bedtools intersect -v` is one option for identifying the unique genes from the older gene model. <https://bedtools.readthedocs.io/en/lates…
Comment: Alien-hunter outputs
by
schlogl
▴ 130
@GenoMax Hope this helps...Thank you
Comment: DESeq2 results function runs very slow on Windows 10
by
ATpoint
68k
Does it go away if you remove the `parallel` from `results()`? After all, it is the `DESeq()` function that is the bottleneck when n is lar…
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
enrique@L:~/bioinformatica/index/prueba$ head -n 997531 GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.gff|tail -n 1 NC_007982.1 Ref…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Chris
▴ 60
Thank you for your help! I got an error that I could not find the solution on the Internet: library(EnhancedVolcano) Loading required…
Comment: HTSeq error processing GFF file
by
barslmn
★ 1.2k
I guess you can try to replace the "?" to a "." Also, you can copy and paste text instead of the screenshots?
Answer: DESeq2 results function runs very slow on Windows 10
by
Istvan Albert
96k
Note the following: https://support.bioconductor.org/p/115415/ it looks like it has to do with the Parallel=TRUE flag
Comment: DESeq2 results function runs very slow on Windows 10
by
GenoMax
125k
> there is a massive difference in performance between them. It still is taking only one minute.
Comment: HTSeq error processing GFF file
by
ibq.enriquepola
• 0
Yes, ![enter image description here][1] [1]: /media/images/76ecd9a7-10c2-4526-9849-062605ca
Answer: How can I convert this pairwise format to fasta?
by
GenoMax
125k
This seems to be the output from `sam2pairwise` program: https://github.com/mlafave/sam2pairwise A quick/dirty way may be $ grep -A 1…
Comment: Which file and data structure is used to create volcano plot from scRNA-Seq expe
by
Basti
★ 1.3k
EnhancedVolcano(CV.markers, x = "avg_log2FC", y = "p_val", lab = rownames(CV.markers), pCutoff = 1e-4, FCcutoff =…
Comment: How to perform multiple comparisons using edgeR?
by
ryandward
• 0
Actually, you get one FDR per gene if you don't loop, and perform the comparisons all at once.
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