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187 results • Page
1 of 4
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Forum:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
43 minutes ago by
tulip
• 0
2
votes
3
replies
225
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 3 hours ago by
Gordon Smyth
★ 7.1k • written 1 day ago by
SHN
▴ 40
4
votes
2
replies
118
views
GRCh38.gmap file
gnomix
gmap
6 hours ago by
lorena9132
▴ 10
0
votes
1
reply
115
views
Association study using SNP data
Association
Allele
Parentage
SNP
updated 7 hours ago by
Mathew
▴ 30 • written 15 hours ago by
drajangirija
• 0
0
votes
0
replies
57
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
filtering
independent
linkage
8 hours ago by
Jautis
▴ 530
2
votes
3
replies
723
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 13 hours ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
2
replies
141
views
creating batch colum for batch correction
batch-correction
combat
updated 10 hours ago by
Ram
43k • written 17 hours ago by
Expert
▴ 10
0
votes
4
replies
224
views
Segmentation error while using a tool
smalt
updated 17 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
Ruqaiya
• 0
0
votes
0
replies
63
views
Help with DGEList function
DGEList
R
updated 10 hours ago by
Ram
43k • written 18 hours ago by
Natali
• 0
0
votes
0
replies
66
views
Homer motif analysis
Homer
19 hours ago by
daffodil
▴ 10
0
votes
1
reply
108
views
HCL database download
database
HCL
human
updated 1 day ago by
GenoMax
142k • written 1 day ago by
sooni
▴ 20
1
vote
1
reply
1.0k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
updated 1 day ago by
lcordeiro
▴ 40 • written 14 months ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
213
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 1 day ago by
chrchang523
10k • written 4 days ago by
8armed
• 0
0
votes
5
replies
263
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 1 day ago by
chrchang523
10k • written 1 day ago by
curious
▴ 750
0
votes
0
replies
88
views
Quetion regarding WGCNA
WGCNA
Network-construction
updated 23 hours ago by
Ram
43k • written 1 day ago by
deepak180001
• 0
0
votes
1
reply
136
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 10 hours ago by
Ram
43k • written 1 day ago by
Rob
▴ 170
0
votes
1
reply
134
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Ximena
• 0
0
votes
1
reply
130
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 23 hours ago by
Ram
43k • written 1 day ago by
Valentina
• 0
0
votes
6
replies
325
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
Erina
• 0
0
votes
1
reply
126
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
kalavattam
▴ 190
0
votes
1
reply
118
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Lada
▴ 30
0
votes
0
replies
93
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
1 day ago by
Emilie
• 0
0
votes
0
replies
90
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
1 day ago by
Javier
• 0
0
votes
1
reply
166
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 22 hours ago by
Thanujay S
• 0 • written 1 day ago by
yahn
• 0
0
votes
0
replies
87
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
1 day ago by
mikemakaveli1
• 0
0
votes
0
replies
88
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 1 day ago by
Ram
43k • written 1 day ago by
M.
▴ 30
0
votes
2
replies
150
views
Raw counts using stringtie
stringtie
RNA-seq
updated 1 day ago by
GenoMax
142k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
85
views
Modify plot R mtDNA indel
plot
mtDNA
R
1 day ago by
marco.barr
▴ 90
0
votes
0
replies
189
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
1 day ago by
NorbertK
• 0
2
votes
2
replies
172
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 10 hours ago by
Ram
43k • written 1 day ago by
carolofharvest
▴ 30
9
votes
9
replies
504
views
High Malat-1 expression in single cell data
single-cell
updated 10 hours ago by
Ram
43k • written 5 days ago by
carolofharvest
▴ 30
0
votes
2
replies
184
views
Downloading older version of a tool
Alignment
tools
1 day ago by
Ruqaiya
• 0
0
votes
0
replies
102
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
1 day ago by
rustykb
▴ 20
1
vote
1
reply
130
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 10 hours ago by
Ram
43k • written 1 day ago by
adi.gershon1
• 0
3
votes
5
replies
223
views
Generating mpileup file using samtools
mpileup
samtools
updated 1 day ago by
Joe
21k • written 1 day ago by
Ruqaiya
• 0
0
votes
5
replies
285
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 1 day ago by
b.contreras.moreira
▴ 180 • written 2 days ago by
JH
• 0
1
vote
3
replies
238
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 1 day ago by
ATpoint
82k • written 2 days ago by
Qi
• 0
0
votes
0
replies
101
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
1 day ago by
Amos Bairoch
▴ 120
2
votes
3
replies
239
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 1 day ago by
dthorbur
★ 1.9k • written 1 day ago by
Vijith
▴ 30
0
votes
0
replies
120
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
2 days ago by
Jeyong
• 0
0
votes
2
replies
703
views
homer not configured properly
Homer
makeTagDirectory
updated 2 days ago by
clairechung112
• 0 • written 23 months ago by
amahdi779
• 0
1
vote
3
replies
226
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 2 days ago by
Alex Reynolds
35k • written 2 days ago by
SJP
• 0
0
votes
0
replies
112
views
Empty table plot using plotGseaTable()
FGSEA
1 day ago by
Chris
▴ 260
0
votes
1
reply
163
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 2 days ago by
anovak
▴ 120 • written 2 days ago by
Hang
• 0
1
vote
3
replies
213
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 2 days ago by
jared.andrews07
★ 16k • written 2 days ago by
yvonneh
▴ 10
3
votes
5
replies
278
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
1 day ago by
Maverick
▴ 10
3
votes
8
replies
6.5k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 2 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
176
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
2 days ago by
dtnondorf
• 0
0
votes
1
reply
202
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 2 days ago by
Chris Dean
▴ 390 • written 2 days ago by
sovrappensiero
▴ 90
1
vote
2
replies
226
views
RNA-seq data for deep learning classification
rna-seq
1 day ago by
yahn
• 0
187 results • Page
1 of 4
Recent Votes
Answer: GRCh38.gmap file
Comment: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: GRCh38.gmap file
Answer: Design matrix Differential expression analysis
A: PCA plot from read count matrix from RNA-Seq
A: PCA plot from read count matrix from RNA-Seq
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Recent Awards •
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Popular Question
to
psm
▴ 130
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Medhat
9.7k
Autobiographer
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Mathew
▴ 30
Commentator
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dsull
★ 6.0k
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drajangirija
• 0
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Thanujay S
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Recent Replies
Comment: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
> When is it recommended to use the design <- cbind(Intercept=1,Group=c(-1,-1,-1,1,1,1)) It is not recommended. No such code appears anywh…
Comment: GRCh38.gmap file
by
lorena9132
▴ 10
Hi Mathew, The .txt files provided in the link differ from the .gmap files, but after several attempts, I succeeded in generating the .gma…
Answer: GRCh38.gmap file
by
Mathew
▴ 30
Hi, I have spent some time searching for a GRCH38 map file for you. I have found a certain publication that uses a hg38 genetic map file…
Answer: Association study using SNP data
by
Mathew
▴ 30
Hi, You asked three questions so I will attempt to help the best I can **What should be the optimal GC score cutoff** It sounds li…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Thank you for your explanation. I am working on the cell lines and I am investigating the effect of the treatment on the expression level, …
Answer: Issues with Mixture file when using CIBERSORTx
by
vjanve
• 0
I ran into same issue of "duplicated gene symbol(s)": 1: In CIBERSORTxFractions(sigmatrix = sigmatrix, mixture = mixture, : 22292 dup…
Comment: creating batch colum for batch correction
by
Expert
▴ 10
Thank you for your response. These samples were collected from the same patient at different time points(day 0, 8 and 18) and these are ind…
Comment: creating batch colum for batch correction
by
ATpoint
82k
Not sure I follow. Can you first of all describe which comparisons you want to make, pretending there was no batch effect at all. Write dow…
Comment: Pindel Segmentation Fault Error
by
Ruqaiya
• 0
This the tool still problematic?
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
Thank you for the advice, i'll keep that in mind.
Comment: Segmentation error while using a tool
by
Ruqaiya
• 0
I am trying to reproduce some bioinformatics data from a research paper-[this paper][1] as i was asked to work on an MRSA bioinfo project, …
Answer: Segmentation error while using a tool
by
Mensur Dlakic
★ 27k
Most likely you didn't do anything wrong. Going by your previous post that you have only 8 GB of RAM, the most likely reason is the lack of…
Comment: Segmentation error while using a tool
by
Thanujay S
• 0
Hey @Ruqaiya! Can you please give more details on why smalt is opted here? According to what I can see, the tool has become obsolete! Why …
Comment: Extracting mutation status from MAF files - TCGA
by
Thanujay S
• 0
Hey! Can you explain the question further? What have you tried?
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
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