Yes, this is it.

Q: Is this book you are looking for?
A: Yes, this is it.
Q: Has she replied to your letter?
A: No, she hasn’t.
Q: Were you out shopping yesterday?
A: Yes, I had.
Q: Had you not gone to cinema?
A: No. I had not.
Q: Had Raman also been studying with you?
A: Yes.
Q: Was your aunt singing at your house?
A: No, it was my sister.
Q: Were you studying English?
A: Yes, I was learning English.
Please correct all.
Thanks.

Q: Is this the book you are looking for?
A: Yes, it is.
Q: Has she replied to your letter?
A: No, she hasn’t.
Q: Were you out shopping yesterday?
A: Yes, I was.
Q: Did you go to the cinema (yesterday)?
A: No, I didn’t.
Q: Had Raman also been studying with you (until you completed the course of study)?
A: Yes, he had.
Q: Was your aunt singing at your house?
A: No, she wasn’t. It was my sister.
Q: Were you studying English?
A: Yes, I was. (No, I was learning English.)

(A mere YES or NO answer will also be acceptable)

Was that your aunt who was singing at your house?

  • that is the only one of the original sentences which needed correction.

Anglophile,
‘Had you not gone to cinema?’
Is the question wrong grammatically?
Please explain.
Thanks.

As a stand-alone sentence, it is not usual. I left out the negator while modifying the original. However, ‘Did you not go to the cinema?’ is more suitable if you just want to refer to the past.
(Note: We use the past perfect tense mainly on two occasions. One is to indicate the ‘past in the past’ as in ‘The thieves had taken to their heels when the police arrived’. The other is ‘to report a present perfect or past simple activity’ as in: He said, “I have visited the Taj Mahal twice”/He said, “I visited the Taj Mahal twice” - both of which may be reported as ‘He said that he had visited the Taj Mahal twice’. For a student the reporting is always ‘remote’. The newspersons have their own style of reporting in order to bring in the effect of importance or immediacy to the reader/listener, though.)

Anglophile,
Q: Had Raman also been studying with you?
I think it is past perfect continuous.
We can use it as a stand alone sentence.
Am I correct?
Please comment.
Thanks.

No, it isn’t incorrect, but as has been explained many times, it is impossible to tell from standalone sentences whether anyone is using the correct tense for their intended meaning.

This is the normal reporting practice: past simple and present prefect & past continuous and present perfect continuous would be changed into past perfect & past perfect continuous respectively. (I have used ‘&’ to avoid confusion.)

Anglophile,
Q1: Had Raman also been studying with you?
Q2: Was Raman also studying with you?
Q1 is in past perfect continuous tense while Q2 is in past continuous tense.
Are both Q1 and Q2 stand alone sentences?
If Q1 is a stand alone sentence, is it acceptable?
Please clarify my doubt. Thanks.

Q1: Had Raman also been studying with you? (Not acceptable; this is ‘past in the past’ so you have to show the other past)
Q2: Was Raman also studying with you? (Acceptable since it is a mere reference to the past simple like the present simple: 'Is Raman also studying with you?)
Q1 is in past perfect continuous tense while Q2 is in past continuous tense. (Correct)
Are both Q1 and Q2 stand alone sentences? (No, only Q2)
If Q1 is a stand alone sentence, is it acceptable? (No, not in this situation where the context is not specific or clear)
(We have a tendency, as I have been observing for decades, to use the past perfect or past perfect continuous just to refer to past simple or past continuous. This is found - on research - to be the result of the influence of our mother tongue. Please stop to examine the context and try to understand the point when you come across the use of these two tense constructions while reading a good article or a narration or a novel or a short story, written by a well-known or educated author, in future.)

(Edited) Meanwhile please check these links which I have googled and found for you: englishtenses.com/node/1036.