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1,000 results • Page
1 of 20
Sort: Rank
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Votes
Replies
0
votes
0
replies
6
views
Practical upper limit for size of DESeq dds object for a powerful desktop
dds
DESeq2
samples
wall
time
24 minutes ago by
Vincent Laufer
★ 3.0k
0
votes
0
replies
9
views
About Bedgraph file basics
Bedgraph
31 minutes ago by
minakshiboruahassam
• 0
0
votes
1
reply
85
views
How to write a Python program that takes the sequences.fasta file and writes N single-sequence FASTA files, called sequence{number}.fasta, each one c…
fasta
python
sequence
updated 4 hours ago by
Pierre Lindenbaum
155k • written 4 hours ago by
Ειρήνη
• 0
0
votes
0
replies
32
views
Cellchat error: data.signaling matrix error when using mouse database (Error in identifyOverExpressedGenes)
Seurat
Cellchat
scRNA
4 hours ago by
Aydin
• 0
0
votes
1
reply
109
views
What are your preferred programs for processing DNA long reads? (de novo assembly)
de
novo
long
assembly
reads
updated 7 hours ago by
Medhat
9.6k • written 10 hours ago by
ashleymb1116
• 0
0
votes
2
replies
108
views
amrfinder not working on loop?
amrfinderplus
updated 11 hours ago by
Pierre Lindenbaum
155k • written 11 hours ago by
Sapphire
• 0
0
votes
0
replies
73
views
How does ncbi-blastP calculate the score ? (Why it is lower than mean-diagonal(blossum62) * length ) ?
protein
alignment
6 hours ago by
Alexander
▴ 110
0
votes
1
reply
621
views
novel miRNA naming(annotation)
snp
RNA-Seq
genome
miRNA
updated 11 hours ago by
Ram
39k • written 2.5 years ago by
zahidhussaindogar113
• 0
1
vote
1
reply
120
views
R ggplot
R
ggplot
updated 11 hours ago by
Ram
39k • written 15 hours ago by
lela2314
• 0
0
votes
0
replies
63
views
Annotation of gene expression TCGA data
tcga
SummarizedExperiment
r
16 hours ago by
atemedorri137798
• 0
0
votes
0
replies
91
views
Why in Heatmap plot my case and control samples of single cell dataset are not well clustered?
cell
single
DESeq2
Heatmap
23 hours ago by
paria
▴ 70
0
votes
2
replies
161
views
How to deal with SRA file without .SRA
SRA
1 day ago by
Andy
▴ 50
0
votes
0
replies
86
views
How does kallisto genomebam handle multi mapping reads?
kallisto
updated 1 day ago by
Ram
39k • written 1 day ago by
bioinfo
▴ 80
1
vote
6
replies
210
views
GISTIC from ASCAT
alteration
copy-number
sequencing
18 hours ago by
Hyper_Odin
▴ 290
8
votes
7
replies
209
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf
VEP
1 day ago by
Jeremy Leipzig
21k
0
votes
0
replies
82
views
using non-matched read counts for differential expression analysis (ncRNA)?
sRNAbench
RNA-seq
expression-matrix
sRNAtoolbox
updated 1 day ago by
Ram
39k • written 1 day ago by
danazeid3
• 0
0
votes
0
replies
92
views
how to ensure that embedding for the new data is initialized based on the embedding of the existing data in UMAP?
UMAP
1 day ago by
Raheleh
▴ 250
0
votes
0
replies
96
views
cannot find genes with abricate and VFDB
abricate
wgs
vfdb
1 day ago by
luciano.g
• 0
1
vote
1
reply
143
views
Filtering content in heatmap to highest values
R
heatmap
ggplot2
1 day ago by
cthangav
▴ 50
5
votes
8
replies
292
views
conda: command not found: gatk.
conda
gatk
1 day ago by
bestone
▴ 20
1
vote
2
replies
379
views
If I execute "AddOrReplaceReadGroups" on a sorted and duplicate-marked .bam file, do I have to re-sort and re-mark duplicates?
picard
AddOrReplaceReadGroups
bam
read-groups
updated 1 day ago by
Ram
39k • written 2 days ago by
javiflaja
• 0
0
votes
0
replies
138
views
Changing gap open and extension penalties in muscle (or any other command line tool that works on mac, really)
multiple-sequence-alignment
updated 1 day ago by
Ram
39k • written 2 days ago by
sodiumnitrate
▴ 20
0
votes
0
replies
147
views
How are the reads assigned to genes in strand-specific RNAseq libraries?
strand-specific
strandness
RNAseq
2 days ago by
Sib
▴ 40
0
votes
1
reply
170
views
GSEA application not launching
GSEA
updated 2 days ago by
GenoMax
130k • written 2 days ago by
Jen
▴ 40
0
votes
0
replies
128
views
Using Tumor Immune Dysfunction and Exclusion (TIDE)
TPM
cancer
r
1 day ago by
JACKY
▴ 100
0
votes
0
replies
128
views
question related to novel mirna file from miRDeep2?
miRDeep2
2 days ago by
kuttibiotech2009
▴ 30
0
votes
0
replies
137
views
How to create a haplotype map?
picard
haplotype
CrosscheckFingerprints
updated 2 days ago by
Ram
39k • written 2 days ago by
jgarces
▴ 30
0
votes
2
replies
187
views
Blast reads classification
NGS
magicblast
blast
updated 2 days ago by
Ram
39k • written 2 days ago by
Giulia.cosenza
▴ 80
4
votes
4
replies
266
views
Normalized counts bulk RNA-seq to DEGs
RNA-seq
updated 2 days ago by
ATpoint
73k • written 2 days ago by
t.ru
▴ 20
0
votes
0
replies
96
views
Required input files for COHCAP
TCGA
Methylation
input
COHCAP
2 days ago by
dilrajkaur766
• 0
0
votes
2
replies
167
views
Chain file for Homo_sapiens_assembly38.fasta to liftover Nebula vcf
hg38
fasta
hg19
chainfile
2 days ago by
berndmann
▴ 10
0
votes
1
reply
145
views
How to remove cloning vector sequence from bacterial assembled genome?
assembly
removal
bacterial
genome
vector
updated 2 days ago by
GenoMax
130k • written 2 days ago by
mathavanbioinfo
▴ 70
0
votes
2
replies
254
views
How do I calculate differential expression for RNA-seq values with the "limma" package and the "ebayes" function?
differential-expression
TPM
GSEA
PANDA
2 days ago by
John
• 0
1
vote
1
reply
131
views
Plotting GO enrichment DATA
R
GO
enrichment-analysis
updated 2 days ago by
Ram
39k • written 2 days ago by
hellokwmin
• 0
0
votes
0
replies
96
views
Popcorn using SNPs with extremely low P-value
Popcorn
SNP
2 days ago by
Apprentice
▴ 160
1
vote
1
reply
162
views
UCSC genome browser
Genome-browser
shannon-entropy
updated 2 days ago by
Ram
39k • written 3 days ago by
Lkhagvadulam
• 0
0
votes
0
replies
96
views
CIBERSORTx hires mode duplicates
CIBERSORT
CIBERSORTx
RNA-seq
bulk
deconvolution
3 days ago by
michaelhojungyoon
• 0
0
votes
0
replies
113
views
Copy Number Alteration and Loss or Heterozygosity
LOH
CNA
copy-number
updated 2 days ago by
Ram
39k • written 3 days ago by
Bogdan
★ 1.3k
0
votes
1
reply
148
views
How to add annotation columns with specific colors to the heatmap?
R
heatmap
RNA-seq
updated 2 days ago by
Ram
39k • written 3 days ago by
ahmad mousavi
▴ 750
0
votes
4
replies
230
views
CellRanger problem
RNA-seq
STAR
scRNA
22 hours ago by
Carlos Eduardo
• 0
0
votes
5
replies
234
views
VCF file CSQ flag
vcf
exome-sequencing
updated 3 days ago by
Ram
39k • written 3 days ago by
Payal
▴ 140
0
votes
0
replies
97
views
normalize for sample size in single cell rna seq cluster frequencies data
scRNAseq
seurat
10x
3 days ago by
chi.delta
▴ 40
1
vote
1
reply
134
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 3 days ago by
GenoMax
130k • written 3 days ago by
saint-even
• 0
0
votes
0
replies
89
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
3 days ago by
dilrajkaur766
• 0
0
votes
0
replies
96
views
m6A-seq input normalisation with RNA-seq
MeRIP-Seq
bamCompare
deepTools
m6A-seq
normalisation
15 hours ago by
Parichitran
• 0
0
votes
1
reply
162
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
updated 3 days ago by
Ram
39k • written 3 days ago by
aaronlogsdon2001
• 0
0
votes
0
replies
90
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
3 days ago by
cate.cevallos
• 0
1
vote
4
replies
246
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 3 days ago by
ATpoint
73k • written 3 days ago by
Zhichao
• 0
0
votes
1
reply
132
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 3 days ago by
ATpoint
73k • written 3 days ago by
f2ff7a46
• 0
0
votes
1
reply
154
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 3 days ago by
ATpoint
73k • written 3 days ago by
t.ru
▴ 20
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how to split multi-fasta file into single fasta file named by header
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155k
get a bed file for your genes and use tabix: tabix --regions genes.bed "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/clinvar…
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I finally solved this with the help of the hmmer devs https://github.com/EddyRivasLab/hmmer/issues/302#issuecomment-1539968198 Firstly yo…
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Yes the documentation for Custom Content is the worst out of all MultiQC docs. I've been intending to rewrite it for a while now. Best bet …
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sounds great! waiting for your findings~
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thank you for sharing your experience!
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9.6k
There is already an article about the topic that was recently published (I was one of the individuals approached to contribute to this arti…
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Apologies - my email address and twitter are listed on my profile page.
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thanks, bro I get the solve of my problem by installing new environment and reinstalling samtools software again.
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Thanks for telling me that, and i apologize for bad explanation because I am beginner user with the site!
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what is the output of the following commands: ls -lah '/home/bvs/neelam/AMRFINDER_hypo/hypothetical_analysis/P_aeruginosa_RP73.fasta' …
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