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1,000 results • Page
1 of 20
Sort: Rank
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Views
Votes
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0
votes
0
replies
1
view
filtering SAM/BAM to remove hits wiht less than x reads aligning
align
bbmap
metagenomics
just now by
Bryan
▴ 10
0
votes
0
replies
12
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
1 hour ago by
tss243
• 0
1
vote
2
replies
77
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 3 hours ago by
ATpoint
78k • written 4 hours ago by
ohtang7
▴ 30
0
votes
0
replies
37
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 3 hours ago by
GenoMax
136k • written 4 hours ago by
sativus
▴ 10
0
votes
0
replies
46
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 5 hours ago by
GenoMax
136k • written 5 hours ago by
PierreGT
• 0
0
votes
0
replies
47
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
5 hours ago by
reaset41
• 0
0
votes
0
replies
39
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
6 hours ago by
jorge.cortes.miranda
• 0
0
votes
1
reply
102
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
updated 6 hours ago by
Nitin Narwade
★ 1.5k • written 8 hours ago by
eamaunders
• 0
1
vote
2
replies
146
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 10 hours ago by
DBScan
▴ 210 • written 14 hours ago by
applepie
• 0
0
votes
2
replies
173
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
updated 10 hours ago by
GenoMax
136k • written 1 day ago by
cook.675
▴ 200
0
votes
1
reply
115
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 7 hours ago by
rpolicastro
12k • written 15 hours ago by
saipra003
▴ 10
0
votes
0
replies
74
views
How to find node Postion and source(sample) ?
vg
16 hours ago by
zhang yi xing
▴ 20
0
votes
3
replies
195
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 9 hours ago by
ATpoint
78k • written 21 hours ago by
DINESHR
• 0
0
votes
0
replies
68
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
16 hours ago by
Richard Fontaine
• 0
2
votes
5
replies
189
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 42 minutes ago by
tshtatland
▴ 170 • written 17 hours ago by
cee28
▴ 20
0
votes
2
replies
278
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 18 hours ago by
cmdcolin
★ 3.4k • written 19 hours ago by
Dylan C-C
• 0
3
votes
4
replies
243
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 10 hours ago by
Nitin Narwade
★ 1.5k • written 21 hours ago by
RNAseqer
▴ 250
0
votes
0
replies
78
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
1 day ago by
rbronste
▴ 420
1
vote
3
replies
221
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 1 day ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
Bine
▴ 50
0
votes
1
reply
132
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
Saurabh
• 0
1
vote
6
replies
295
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
14 hours ago by
CTLong
▴ 10
2
votes
1
reply
138
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
jiyoung
▴ 20
0
votes
0
replies
90
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
1 day ago by
Smriti
▴ 10
1
vote
4
replies
242
views
Bowtie mapping for single_end read
bowtie
1 day ago by
Rita
• 0
0
votes
0
replies
84
views
String App in Cytoscape
App
String
cytoscape
1 day ago by
hellokwmin
• 0
0
votes
0
replies
100
views
missing region in the process of annotation
annotatr
minfi
1 day ago by
Aki
▴ 10
1
vote
0
replies
91
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
0
votes
6
replies
303
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
2 hours ago by
tw_140
• 0
9
votes
16
replies
684
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
20 hours ago by
analyst
▴ 10
0
votes
0
replies
87
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
2 days ago by
user230613
▴ 350
0
votes
4
replies
239
views
Species coverage in the NCBI protein NR database ?
NR
updated 2 days ago by
Istvan Albert
99k • written 2 days ago by
HERMAN
▴ 10
0
votes
0
replies
95
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
2 days ago by
Jaykishan
• 0
0
votes
1
reply
145
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 7 hours ago by
CTLong
▴ 10 • written 2 days ago by
e.iich
• 0
0
votes
3
replies
215
views
merged rs number information
merged
dbsnp
1 day ago by
sskimvd
• 0
1
vote
1
reply
150
views
Beginner differential methylation analysis
Methylation
updated 2 days ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
225
views
EnhancedVolcano underrepresenting DEGs
R
updated 1 day ago by
Kevin Blighe
86k • written 3 days ago by
jabbari.parnian
▴ 30
0
votes
0
replies
104
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
3 days ago by
jiazheng_lin
• 0
0
votes
0
replies
117
views
Negative F statistics for sex check in plink
plink
check
sex
3 days ago by
kl
▴ 10
0
votes
1
reply
185
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 1 day ago by
Arup Ghosh
3.2k • written 3 days ago by
Mehwish
▴ 10
0
votes
1
reply
236
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 4 days ago by
GenoMax
136k • written 4 days ago by
subhiksha
• 0
0
votes
3
replies
332
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 4 days ago by
ATpoint
78k • written 5 days ago by
manuelmourato25
• 0
0
votes
0
replies
222
views
The number of variations in the pan-genome is reduced compared to the variations in the input VCF file
vg
5 days ago by
Wenke
• 0
0
votes
3
replies
298
views
Annovar - Annotated file cells show string
annovar
5 days ago by
Roshan
• 0
0
votes
1
reply
236
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 4 days ago by
GenoMax
136k • written 5 days ago by
Soumajit
▴ 40
0
votes
0
replies
155
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
5 days ago by
bioinfo
▴ 60
0
votes
0
replies
155
views
Seeking Advice on WGCNA for Nematode Sexual Dimorphism
WGCNA
Worms
RNA-Seq
5 days ago by
kdca
• 0
0
votes
3
replies
267
views
labelling the clusters from the CD4 T cell scRNAseq data
scRNAseq
5 days ago by
Sara
▴ 230
0
votes
0
replies
867
views
Any tools for finding the telomere sequences / lengths directly for nanopore sequencing reads without any prior knowledge of the organism
genomics
telomeres
reads
5 days ago by
Mark
• 0
0
votes
0
replies
151
views
not best k value found
de
assemblly
assembly
novo
kmergenie
5 days ago by
shaileshdesai76
• 0
0
votes
0
replies
159
views
Multi-mapped reads in Ribo-Seq data, discard or keep?
STAR
ribo-seq
multi-mapped
rna-seq
TE
5 days ago by
Carmen
• 0
1,000 results • Page
1 of 20
Recent Votes
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Recent Replies
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R
by
ohtang7
▴ 30
Thank you!! I really appreciate your help.
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